heterotachy.py
Remove the most heterotachious sites from a phylogenomic supermatrix in a stepwise fashion.
heterotachy.py -tr <input_tree> -m <input_matrix> [OPTIONS]
Required arguments:
-tr
,--tree <input.tre>
Path to tree in Newick format-m
,--matrix <matrix.fas|nex|phy>
Path to supermatrix
Optional arguments:
-s
,--step_size <N>
Size of removal step (i.e., 1000 sites removed) to exhaustion.- Default:
3000
- Default:
-f
,--out_format <format>
Desired format of the output matrices.- Options:
fasta
,nexus
,phylip
(names truncated at 10 characters) orphylip-relaxed
(names are not truncated) - Default:
fasta
- Options:
-o
,--output <out_dir>
Path to user-defined output directory.- Default:
./heterotachy_out_<M.D.Y>
- Default:
-h
,--help
Show this help message and exit.
Default heterotachy.py
output
- a directory
heterotachy_out_<M.D.Y>
that contains:slow.tre
- tree file in Newick format containing a tree pruned from the input tree and contains only taxa determined to be slow-evolving.fast.tre
- tree file in Newick format containing a tree pruned from the input tree and contains only taxa determined to be fast-evolving.slow.phy
- phylip formatted file containing only slow-evolving taxa.fast.phy
- phylip formatted file containing only fast-evolving taxa.slow.dist_est.ctl
- control file to be used by dist_est for slow-evolving taxa.fast.dist_est.ctl
- control file to be used by dist_est for fast-evolving taxa.slow.DE.dat
&& - an output of the dist_est operation onslow.phy
andslow.tre
.slow.rate_est.dat
&& - an output of the dist_est operation onslow.phy
andslow.tre
.fast.DE.dat
&& - an output of the dist_est operation onfast.phy
andfast.tre
.fast.rate_est.dat
&& - an output of the dist_est operation onfast.phy
andfast.tre
.- a subdirectory
steps_<N>
(N=step size) that contains the files:step<0-N>.phy
- phylip formatted matrix files with N less sites than the previous step to exhaustion.
&& These are standard dist_est input/output files. See the dist_est documentation for a more detailed explanation of their contents.