rtc_binner.py
Bin orthologs based on relative tree certainty score and construct supermatrices from the bins.
rtc_binner.py [OPTIONS] -i <input_dir>
Required arguments:
-i
,--input <input_dir>
Path to directory containing single gene trees built from only orthologs, corresponding bootstrap value files, and corresponding alignments.
Optional arguments:
--in_format <format>
Format of the input files- Options:
fasta
,nexus
,phylip
(names truncated at 10 characters), orphylip-relaxed
(names are not truncated) - Default:
fasta
- Options:
--out_format <format>
Desired format of the output files- 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:
./rtc_binner_out_<M.D.Y>
- Default:
-p
,--prefix <prefix>
Prefix of input files- Default:
NONE
- Example:
path/to/input/prefix*
- Default:
-s
,--suffix <suffix>
Suffix of input files- Default:
NONE
- Example:
path/to/input/*suffix
- Default:
-h
,--help
Show this help message and exit
rtc_binner.py
output:
- a directory
./rtc_binner_out_<M.D.Y>
with 7 subdirectories:matrix_constructor25/
that contains:- supermatrix (matrix, stats, and indices) of the top 25% RTC scored orthologs
matrix_constructor50/
that contains:- supermatrix (matrix, stats, and indices) of the top 50% RTC scored orthologs
matrix_constructor75/
that contains:- supermatrix (matrix, stats, and indices) of the top 75% RTC scored orthologs
rtc25/
that contains:- alignments of the top 25% RTC scored orthologs
rtc50/
that contains:- alignments of the top 50% RTC scored orthologs
rtc75/
that contains:- alignments of the top 75% RTC scored orthologs