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v.250331
Fixes by Michael Hiller
- nuc vs. aa detection and information passed to Mafft
Fixes by Martin Larralde
- speed ups by removal of unnecessary calls
v.170703
Many changes not previously uploaded to GitHub, for example:
- guide tree inference with FastTree
- ancestral states with RAxML
- possible re-estimation of branch lengths
v.170427
Changes by Nikolai Hecker
- make the temp files thread safe
- fix a compile issue with GCC 6.2.0
- reduce the information written to stdout; disable with "-verbose"
v.150803
- force linear order of alignment anchors
- convert multifurcating trees to bifurcating ones
- finish despite BppAncestor failing
v.140603
- now avoids crashes due to weird sequence names
- now (codon) ancestral reconstructio also for translated alignments
- new option '-njgaps' to consider gaps as mismatches for NJ distances
v.140110
- a fix for the external tool paths
v.131211
- search order for external tools changed: use own one first
- '-nobbpa' to run without BppAncestors (even when available)
- a fix for rare crashes due to overly long branch lengths
v.131119
- ancestor inference for translated alignments of DNA sequences
- new option '-treeonly'
v.130820
- disabled copmutation of alignment score for the guide tree alignment
- more information about iteration with a user-provided tree
- workaround for a BppAncestor bug causing incomplete last codon
- path to other binaries no more affected by renaming of the program file
v.130708
- Significant bug fixes -- update *strongly* recommended:
* option -F was mistakenly turned off by the new iterative approach
* without option -F, ancestor reconstruction (and scoring) were incorrect
v.130410
- More information about optimization score and fix for last alignment
- Minor fixes on alignment conversion and use of external models
v.130129
- Introduced alignment score and automatic iteration to maximise the score
- Changed interface for the analysis input and output
- New output: inferred evolutionary events per branch
v.121218
- More detailed information about unmatching names. New option "-prunedata".
v.121212
- Support for some NHX tags.
v.121210
- Fixed underflow errors affecting ancestral reconstruction of large
alignments.
v.121018
- Ancestral sequences can differently indicate insertions and deletions.
- Can update an alignment, recomputing nodes with tag "[&&NHX:XN=realign]"
v.121002
- Alignment merge now accepts trees such as "(t1:#.#,t2:#.#);".
Provided with "-t=filename" or "-tree=tree-string".
v.120827
- All files now under the GPL licence.
v.120814
- Can now also merge "alignments" of one sequence
- New option '-mergedist=#' to define the distance for two alignments
v.120717
- All input data now converted to upper-case.
v.120716
- Fixed the translated alignment (been broken in recent clean up)
- Fixed the output order of ancestral sequences
v.120712
- For codon alignment, MAFFT guide tree now with protein sequences
(fixes several issues with codon alignment)
v.120626
- Guide tree estimation from a MAFFT alignment
- Merge of two pre-defined alignments
- Support for Exonerate and MAFFT on Windows
- Clean up of some code
v.111130
- Exonerate anchoring now also for guidetree computation. Experimental!
v.111129
- Allow guide trees with no branch lengths. Default branch length is 0.1;
use -fixedbranches=# to change.
- Removed the dependency to boost libraries.
v.111013
- First update in Google Code
- Alignment speed ups with Exonerate anchoring.
v.101018
- Last version before migration to Google Code
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