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ESPOCA - Estimate Selective Pressure on Codon Alignments
This directory contains example input files:
example.fa codon alignment file in multi fasta format
tree.nwk phylogenetic tree file in newick format with branch length
Example Command:
espoca --species=fly --alnfile=example.fa --treefile=tree.nwk
Output:
#
# ESPOCA - Estimate Selective Preassure on Codon Alignments.
#
# Description of the table columns:
# ali_pos ref_pos AS_ref Pr(w>1) post_mean +- SE_for_w num_subst
# 1. ali_pos position of codon site in the alignment
# 2. ref_pos position of codon in reference species (first species in the alignment file), -1 if gap in reference
# 3. AS_ref amino acid of reference sequence at ref_pos
# 4. Pr(w>1) probability of omega > 1 at alipos (*: Pr(w>1) > 0.90, **: Pr(w>1) > 0.95)
# 5. post_mean posterior mean estimate of omega at ali_pos
# 6. SE_for_w standard deviation of omega at ali_pos
# 7. num_subst number of substitution calculated by the Fitch algorithm
ali_pos ref_pos AS_ref Pr(w>1) post_mean +- SE_for_w num_subst
0 0 M 0.249188 0.814206 +- 0.362779 0
1 1 I 0.489331 1.22654 +- 0.606094 0
2 2 M 0.278273 0.865713 +- 0.391453 0
3 -1 - 0.375208 1.02205 +- 0.387321 2
4 -1 - 0.510076 1.22844 +- 0.484266 3
5 -1 - 0.520523 1.27867 +- 0.620131 1
6 -1 - 0.42937 1.12316 +- 0.538455 0
7 -1 - 0.479403 1.20924 +- 0.595183 0
8 3 M 0.249188 0.814206 +- 0.362779 0
9 4 I 0.495239 1.23701 +- 0.613456 0
10 5 M 0.270909 0.852741 +- 0.384469 0
11 6 M 0.249188 0.814206 +- 0.362779 0
12 7 L 0.592153 1.41444 +- 0.726155 0
13 8 L 0.556823 1.34642 +- 0.677838 0
14 9 Y 0.286488 0.879981 +- 0.3289 1
15 10 L 0.556823 1.34642 +- 0.677838 0
16 11 A 0.48803 1.22396 +- 0.594927 1
17 12 K 0.475777 1.20248 +- 0.578938 1
18 13 N 0.417649 1.10366 +- 0.53543 0
19 -1 - 0.489014 1.22646 +- 0.609409 0
20 14 * 0.604201 1.18131 +- 0.528847 0
# posterior mean estimate of omega for whole alignment : 0.543365
# total time: 4.73954s
# command line:
# espoca --species=fly --alnfile=example.fa --treefile=tree.nwk
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