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|
test_AlignIO
Testing reading clustal format file Clustalw/cw02.aln with 1 alignments
Alignment 0, with 2 sequences of length 601
MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVN...SVV gi|4959044|gb|AAD34209.1|AF069
---------MSPQTETKASVGFKAGVKEYKLTYYTP...--- gi|671626|emb|CAA85685.1|
* *: :: :. :* : :. ... clustal_consensus
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/opuntia.aln with 1 alignments
Alignment 0, with 7 sequences of length 156
TTTTTTT alignment column 0
AAAAAAA alignment column 1
TTTTTTT alignment column 2
AAAAAAA alignment column 3
CCCCCCC alignment column 4
||||||| ...
AAAAAAA alignment column 155
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/hedgehog.aln with 1 alignments
Alignment 0, with 5 sequences of length 447
M---- alignment column 0
F---- alignment column 1
N---- alignment column 2
L---- alignment column 3
V---- alignment column 4
||||| ...
---SS alignment column 446
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/odd_consensus.aln with 1 alignments
Alignment 0, with 2 sequences of length 687
------------------------------------...TAG AT3G20900.1-CDS
ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGT...TAG AT3G20900.1-SEQ
...*** clustal_consensus
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-SEQ'), possibly due to truncation
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-SEQ'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/protein.aln with 1 alignments
Alignment 0, with 20 sequences of length 411
-M------------------ alignment column 0
-T------------------ alignment column 1
-V------------------ alignment column 2
-L-----------------M alignment column 3
-E---------------MMS alignment column 4
|||||||||||||||||||| ...
-------------------T alignment column 410
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'gi|1377497' (originally 'gi|13774975|gb|AAK39115.1|AF35'), possibly due to truncation
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Failed: Repeated name 'gi|1377497' (originally 'gi|13774975|gb|AAK39115.1|AF35'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/promals3d.aln with 1 alignments
Alignment 0, with 20 sequences of length 414
MMMMMMMMMMMMMMMM-M-- alignment column 0
-----------------T-- alignment column 1
-----------------V-- alignment column 2
-----------------L-- alignment column 3
-S---------------E-- alignment column 4
|||||||||||||||||||| ...
-T------------------ alignment column 413
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'gi_1393639' (originally 'gi_13936397_dbj_BAB47195.'), possibly due to truncation
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Failed: Repeated name 'gi_1393639' (originally 'gi_13936397_dbj_BAB47195.'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta format file GFF/multi.fna with 1 alignments
Alignment 0, with 3 sequences of length 8
ACGTCGCG test1
GGGGCCCC test2
AAACACAC test3
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading nexus format file Nexus/test_Nexus_input.nex with 1 alignments
Alignment 0, with 9 sequences of length 48
AAAAAAAAc alignment column 0
-----c?tc alignment column 1
CCCCCCCCc alignment column 2
--c-?a-tc alignment column 3
GGGGGGGGc alignment column 4
||||||||| ...
tt--?ag?c alignment column 47
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Failed: Whitespace not allowed in identifier: t2 the name
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading nexus format file Nexus/codonposset.nex with 1 alignments
Alignment 0, with 2 sequences of length 22
AAAAAGGCATTGTGGTGGGAAT Aegotheles
?????????TTGTGGTGGGAAT Aerodramus
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading stockholm format file Stockholm/simple.sth with 1 alignments
Alignment 0, with 2 sequences of length 104
UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCA...UGU AP001509.1
AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGA...GAU AE007476.1
.................<<<<<<<<...<<<<<<<....... secondary_structure
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading stockholm format file Stockholm/funny.sth with 1 alignments
Alignment 0, with 6 sequences of length 43
MMMEEE alignment column 0
TQIVVV alignment column 1
CHEMMM alignment column 2
RVALLL alignment column 3
ASDTTT alignment column 4
|||||| ...
SYSEEE alignment column 42
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/reference_dna.phy with 1 alignments
Alignment 0, with 6 sequences of length 13
CCTTCG alignment column 0
GGAAAG alignment column 1
ATAAAC alignment column 2
TTTTAA alignment column 3
GAGGAG alignment column 4
|||||| ...
CTTTTC alignment column 12
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Failed: Whitespace not allowed in identifier: B. virgini
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/reference_dna2.phy with 1 alignments
Alignment 0, with 6 sequences of length 39
CCTTCG alignment column 0
GGAAAG alignment column 1
ATAAAC alignment column 2
TTTTAA alignment column 3
GAGGAG alignment column 4
|||||| ...
CTTTTC alignment column 38
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Failed: Whitespace not allowed in identifier: B. virgini
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/hennigian.phy with 1 alignments
Alignment 0, with 10 sequences of length 40
CCCCCAAAAA alignment column 0
AAAAACCCCC alignment column 1
CCCAAAAAAA alignment column 2
AAACCAAAAA alignment column 3
CCAAAAAAAA alignment column 4
|||||||||| ...
AAAAAAAAAA alignment column 39
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/horses.phy with 1 alignments
Alignment 0, with 10 sequences of length 40
AACCCCCCCC alignment column 0
AAAACCCCCC alignment column 1
AAAAAAAAAC alignment column 2
ACAAAAAAAA alignment column 3
ACACCCCCCC alignment column 4
|||||||||| ...
AAAAAAAAAA alignment column 39
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Failed: Whitespace not allowed in identifier: M. secundu
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/random.phy with 1 alignments
Alignment 0, with 10 sequences of length 40
CAAAACAAAC alignment column 0
AACAACCACC alignment column 1
CAAAACAAAA alignment column 2
ACAACACACA alignment column 3
CCAAAACCAA alignment column 4
|||||||||| ...
AAAAAAAAAA alignment column 39
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/interlaced.phy with 1 alignments
Alignment 0, with 3 sequences of length 384
-----MKVILLFVLAVFTVFVSS-------------...I-- CYS1_DICDI
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPV...VAA ALEU_HORVU
------MWATLPLLCAGAWLLGV--------PVCGA...PLV CATH_HUMAN
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/interlaced2.phy with 1 alignments
Alignment 0, with 4 sequences of length 131
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPG...SHE IXI_236
TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT-...SHE IXI_237
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip-relaxed format file ExtendedPhylip/primates.phyx with 1 alignments
Alignment 0, with 12 sequences of length 898
AAAAAAAAAAAA alignment column 0
AAAAAAAAAAAA alignment column 1
GGGGGGGGGGGG alignment column 2
TCCCCCCCCCCC alignment column 3
TTTTTTTTTTTT alignment column 4
|||||||||||| ...
TTTTTTTTTTTT alignment column 897
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip-sequential format file Phylip/sequential.phy with 1 alignments
Alignment 0, with 3 sequences of length 384
-----MKVILLFVLAVFTVFVSS-------------...I-- CYS1_DICDI
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPV...VAA ALEU_HORVU
------MWATLPLLCAGAWLLGV--------PVCGA...PLV CATH_HUMAN
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip-sequential format file Phylip/sequential2.phy with 1 alignments
Alignment 0, with 4 sequences of length 131
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPG...SHE IXI_236
TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT-...SHE IXI_237
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/alignret.txt with 1 alignments
Alignment 0, with 4 sequences of length 131
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPG...SHE IXI_236
TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT-...SHE IXI_237
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/needle.txt with 5 alignments
Alignment 0, with 2 sequences of length 124
KILIVDD----QYGIRILLNEVFNKEGYQTFQAANG...--- ref_rec
-VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDG...GET gi|94968718|receiver
Alignment 1, with 2 sequences of length 119
KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQAL...--- ref_rec
-ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRAL...LKR gi|94968761|receiver
Alignment 2, with 2 sequences of length 120
-KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQA...--- ref_rec
LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAA...HKE gi|94967506|receiver
...
Alignment 4, with 2 sequences of length 125
KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQAL...--- ref_rec
TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEAL...KRQ gi|94970041|receiver
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/needle_asis.txt with 1 alignments
Alignment 0, with 2 sequences of length 3653
TATTTTTTGGATTTTTTTCTAGATTTTCTAGGTTAT...GAA asis
------------------------------------...GAA asis
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'phylip-relaxed' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'phylip-sequential' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'stockholm' format
Failed: Duplicate record identifier: asis
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/water.txt with 1 alignments
Alignment 0, with 2 sequences of length 131
TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/water2.txt with 1 alignments
Alignment 0, with 2 sequences of length 18
CGTTTGAGT-CTGGGATG asis
CGTTTGAGTACTGGGATG asis
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'phylip-relaxed' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'phylip-sequential' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'stockholm' format
Failed: Duplicate record identifier: asis
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/matcher_simple.txt with 1 alignments
Alignment 0, with 2 sequences of length 16
GPPPQSPDENRAGESS AF069992_1
GVPPEEAGAAVAAESS CAA85685.1
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/matcher_pair.txt with 5 alignments
Alignment 0, with 2 sequences of length 145
LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP...SKY HBA_HUMAN
LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYP...HKY HBB_HUMAN
Alignment 1, with 2 sequences of length 13
KKVADALTNAVAH HBA_HUMAN
QKVVAGVANALAH HBB_HUMAN
Alignment 2, with 2 sequences of length 18
KLRVDPVNFKLLSHCLLV HBA_HUMAN
KVNVDEVGGEALGRLLVV HBB_HUMAN
...
Alignment 4, with 2 sequences of length 10
VKAAWGKVGA HBA_HUMAN
VQAAYQKVVA HBB_HUMAN
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/emboss_pair_aln_full_blank_line.txt with 1 alignments
Alignment 0, with 2 sequences of length 1450
GGCAGGTGCATAGCTTGAGCCTAGGAGTTCAAGTCC...AAA hg38_chrX_131691529_131830643_47210_48660
G--------------------------TTCAAGGCC...AAA mm10_chrX_50555743_50635321_27140_27743
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output001.m10 with 4 alignments
Alignment 0, with 2 sequences of length 108
SGSNT-RRRAISRPVRLTAEED---QEIRKRAAECG...LSR gi|10955263|ref|NP_052604.1|
AGSGAPRRRGSGLASRISEQSEALLQEAAKHAAEFG...LSR gi|152973457|ref|YP_001338508.1|
Alignment 1, with 2 sequences of length 64
AAECGKTVSGFLRAAALGKKVNSLTDDRVLKEV-MR...AIT gi|10955263|ref|NP_052604.1|
ASRQGCTVGG--KMDSVQDKASDKDKERVMKNINIM...TLT gi|152973588|ref|YP_001338639.1|
Alignment 2, with 2 sequences of length 38
MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIE gi|10955264|ref|NP_052605.1|
IKKDLGVSFLKLKNREKTLIVDALKKKYPVAELLSVLQ gi|152973462|ref|YP_001338513.1|
Alignment 3, with 2 sequences of length 43
SELHSKLPKSIDKIHEDIKKQLSC-SLIMKKIDVEM...TYC gi|10955265|ref|NP_052606.1|
SRINSDVARRIPGIHRDPKDRLSSLKQVEEALDMLI...EYC gi|152973545|ref|YP_001338596.1|
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output002.m10 with 6 alignments
Alignment 0, with 2 sequences of length 88
SGSNTRRRAISRPVR--LTAEEDQEIRKRAAECG-K...AEV gi|10955263|ref|NP_052604.1|
SQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGRK...VQV gi|162139799|ref|NP_309634.2|
Alignment 1, with 2 sequences of length 53
EIRKRAAECGKTVSGFLRAAA-LGKKV----NSLTD...KKL gi|10955263|ref|NP_052604.1|
EIKPRGTSKGEAIAAFMQEAPFIGRTPVFLGDDLTD...VKI gi|15831859|ref|NP_310632.1|
Alignment 2, with 2 sequences of length 92
SEFFSKIESDLKKKKSKGDVFFDLIIPNG-----GK...ATS gi|10955264|ref|NP_052605.1|
TELNSELAKAMKVDAQRG-AFVSQVLPNSSAAKAGI...QSS gi|15829419|ref|NP_308192.1|
...
Alignment 5, with 2 sequences of length 157
QYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIASLIN...REI gi|10955265|ref|NP_052606.1|
EFIRLLSDHDQFEKDQISELTVAANALKLEVAK--N...KKV gi|15833861|ref|NP_312634.1|
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output003.m10 with 3 alignments
Alignment 0, with 2 sequences of length 55
ISISNNKDQYEELQKEQGERDLKTVDQLVRIAAAGG...IAA gi|152973837|ref|YP_001338874.1|
VRLTAEEDQ--EIRKRAAECG-KTVSGFLRAAALGK...LGA gi|10955263|ref|NP_052604.1|
Alignment 1, with 2 sequences of length 22
DDAEHLFRTLSSR-LDALQDGN gi|152973840|ref|YP_001338877.1|
DDRANLFEFLSEEGITITEDNN gi|10955265|ref|NP_052606.1|
Alignment 2, with 2 sequences of length 63
VFGSFEQPKGEHLSGQVSEQ--RDTAFADQNEQVIR...QAM gi|152973841|ref|YP_001338878.1|
VYTSFN---GEKFSSYTLNKVTKTDEYNDLSELSAS...KGI gi|10955264|ref|NP_052605.1|
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output004.m10 with 1 alignments
Alignment 0, with 2 sequences of length 102
AAAAAAGATAAAAAATATCAAATAGAAGCAATAAAA...TCA ref|NC_002127.1|:c1351-971
AGAGAAAATAAAACAAGTAATAAAATATTAATGGAA...ACA ref|NC_002695.1|:1970775-1971404
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'ref|NC_002' (originally 'ref|NC_002695.1|:1970775-1971404'), possibly due to truncation
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Failed: Repeated name 'ref|NC_002' (originally 'ref|NC_002695.1|:1970775-1971404'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output005.m10 with 1 alignments
Alignment 0, with 2 sequences of length 110
IKNKDKTLFIVYAT-DIYSPSEFFSKIESDLKKKKS...LSK gi|10955264|ref|NP_052605.1|
IKDELPVAFCSWASLDLECEVKYINDVTSLYAKDWM...MSE gi|10955282|ref|NP_052623.1|
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output006.m10 with 1 alignments
Alignment 0, with 2 sequences of length 131
GCAACGCTTCAAGAACTGGAATTAGGAACCGTGACA...CAT query
GCAACGCTTCAAGAACTGGAATTAGGAACCGTGACA...CAT gi|116660610|gb|EG558221.1|EG558221
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output007.m10 with 9 alignments
Alignment 0, with 2 sequences of length 108
SGSNT-RRRAISRPVRLTAEED---QEIRKRAAECG...LSR gi|10955263|ref|NP_052604.1|
AGSGAPRRRGSGLASRISEQSEALLQEAAKHAAEFG...LSR gi|152973457|ref|YP_001338508.1|
Alignment 1, with 2 sequences of length 64
AAECGKTVSGFLRAAALGKKVNSLTDDRVLKEV-MR...AIT gi|10955263|ref|NP_052604.1|
ASRQGCTVGG--KMDSVQDKASDKDKERVMKNINIM...TLT gi|152973588|ref|YP_001338639.1|
Alignment 2, with 2 sequences of length 45
EIRKRAAECGKTVSGFLRAAA-----LGKKVNSLTD...VMR gi|10955263|ref|NP_052604.1|
ELVKLIADMGISVRALLRKNVEPYEELGLEEDKFTD...MLQ gi|152973480|ref|YP_001338531.1|
...
Alignment 8, with 2 sequences of length 64
ISGTYKGIDFLIKLMPSGGNTTIGRASGQNNTYFDE...FSD gi|10955265|ref|NP_052606.1|
IDGVITAFD-LRTGMNISKDKVVAQIQGMDPVW---...YPD gi|152973505|ref|YP_001338556.1|
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output008.m10 with 12 alignments
Alignment 0, with 2 sequences of length 65
LQHRHPHQQQQQQQQQQQQQQQQQQQQQQQQQQQH-...QML sp|Q9NSY1|BMP2K_HUMAN
IPHQLPHALRHRPAQEAAHASQLHPAQPGCGQPLHG...GLL gi|283855822|gb|GQ290312.1|
Alignment 1, with 2 sequences of length 201
GPEIL---LGQ-GPPQQPPQQHRVLQQLQQGDWRLQ...NRS sp|Q9NSY1|BMP2K_HUMAN
GPELLRALLQQNGCGTQPLRVPTVLPG*AMAVLHAG...QKS gi|57163782|ref|NM_001009242.1|
Alignment 2, with 2 sequences of length 348
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQ...APA sp|P08100|OPSD_HUMAN
MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQ...APA gi|57163782|ref|NM_001009242.1|
...
Alignment 11, with 2 sequences of length 31
AQQQESATTQKAEKEVTRMVIIMVIAFLICW sp|P08100|OPSD_HUMAN
SQQIRNATTMMMTMRVTSFSAFWVVADSCCW gi|283855822|gb|GQ290312.1|
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt with 1 alignments
Alignment 0, with 16 sequences of length 298
MMMMMMMMMMMMMMMM alignment column 0
EEEEEEETEEEENEEE alignment column 1
NNNNNNNAEEEEQRKK alignment column 2
--------DEEEEE-- alignment column 3
--------KKKKKK-- alignment column 4
|||||||||||||||| ...
HHHHHHH-AAAAL-R- alignment column 297
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading pir format file NBRF/clustalw.pir with 1 alignments
Alignment 0, with 2 sequences of length 2527
------------------------------------...--- 804Angiostrongylus_cantonensis
------------------------------------...--- 815Parelaphostrongylus_odocoil
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading maf format file MAF/humor.maf with 2 alignments
Alignment 0, with 3 sequences of length 5486
gcacagcctttactccctgactgcgtttatattctg...CCG NM_006987
gcacagcctttactccctgactgcgtttatattctg...TTG mm3
gcacagcctttactccctgactgcgtttatattctg...CCG rn3
Alignment 1, with 3 sequences of length 5753
tttgtccatgttggtcaggctggtctcgaactcccc...GGT NM_018289
tttgtccatgttggtcaggctggtctcgaactcccc...GGT mm3
tttgtccatgttggtcaggctggtctcgaactcccc...GGT rn3
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading maf format file MAF/bug2453.maf with 3 alignments
Alignment 0, with 5 sequences of length 42
AAA-- alignment column 0
AAAAA alignment column 1
AAAAA alignment column 2
---T- alignment column 3
GGGGG alignment column 4
||||| ...
GGGGG alignment column 41
Alignment 1, with 5 sequences of length 6
TTTTt alignment column 0
AAAAa alignment column 1
AAAAa alignment column 2
AAAAg alignment column 3
GGGGg alignment column 4
||||| ...
AAAAa alignment column 5
Alignment 2, with 4 sequences of length 13
gcagctgaaaaca hg16.chr7
gcagctgaaaaca panTro1.chr6
gcagctgaaaaca baboon
ACAGCTGAAAATA mm4.chr6
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Testing reading maf format file MAF/ucsc_test.maf with 3 alignments
Alignment 0, with 5 sequences of length 42
AAA-- alignment column 0
AAAAA alignment column 1
AAAAA alignment column 2
---T- alignment column 3
GGGGG alignment column 4
||||| ...
GGGGG alignment column 41
Alignment 1, with 5 sequences of length 6
TTTTt alignment column 0
AAAAa alignment column 1
AAAAa alignment column 2
AAAAg alignment column 3
GGGGg alignment column 4
||||| ...
AAAAa alignment column 5
Alignment 2, with 4 sequences of length 13
gcagctgaaaaca hg16.chr7
gcagctgaaaaca panTro1.chr6
gcagctgaaaaca baboon
ACAGCTGAAAATA mm4.chr6
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Testing reading maf format file MAF/ucsc_mm9_chr10.maf with 48 alignments
Alignment 0, with 2 sequences of length 164
TCATAGGTATTTATTTTTAAATATGGTTTGCTTTAT...GTT mm9.chr10
TCACAGATATTTACTATTAAATATGGTTTGTTATAT...GTT oryCun1.scaffold_133159
Alignment 1, with 4 sequences of length 466
AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGC...CTG mm9.chr10
AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTC...TTC ponAbe2.chr6
AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTC...TTC panTro2.chr6
AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTC...TTC hg18.chr6
Alignment 2, with 5 sequences of length 127
TTTTT alignment column 0
GGGGG alignment column 1
GGGGG alignment column 2
GGGGG alignment column 3
TTTTC alignment column 4
||||| ...
CCCCC alignment column 126
...
Alignment 47, with 6 sequences of length 46
TTTTTT alignment column 0
GGGGGG alignment column 1
TTTTTT alignment column 2
TTTTTT alignment column 3
TGGGAT alignment column 4
|||||| ...
tTTTT- alignment column 45
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Testing reading mauve format file Mauve/simple.xmfa with 5 alignments
Alignment 0, with 2 sequences of length 5670
ATATTAGGTTTTTACCTACCCAGGAAAAGCCAACCA...AAT 1/0-5670
ATATTAGGTTTTTACCTACCCAGGAAAAGCCAACCA...AAT 2/0-5670
Alignment 1, with 2 sequences of length 4420
GAACATCAGCACCTGAGTTGCTAAAGTCATTTAGAG...CTC 1/5670-9940
GAACATCAGCACCTGAGTTGCTAAAGTCATTTAGAG...CTC 2/7140-11410
Alignment 2, with 1 sequences of length 4970
TCTACCAACCACCACAGACATCAATCACTTCTGCTG...GAC 1/9940-14910
...
Alignment 4, with 1 sequences of length 1470
ATTCGCACATAAGAATGTACCTTGCTGTAATTTATA...ATA 2/11410-12880
Checking can write/read as 'clustal' format
Checking can write/read as 'maf' format
Checking can write/read as 'mauve' format
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-relaxed' format
Checking can write/read as 'phylip-sequential' format
Checking can write/read as 'stockholm' format
Finished tested reading files
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