EasySpeciesTree
Easily construct the ML species tree with single-copy gene shared by different species.
Install / Use
/learn @dongwei1220/EasySpeciesTreeREADME
EasySpeciesTree
Easily construct the ML species tree with all single-copy genes shared by different species
Usage: EasySpeciesTree [-h] -in1 INPUT1 -in2 INPUT2 -in3 INPUT3 -in4 INPUT4
[-t THREAD] [-nb BOOTSTRAP] [-m MODEL]
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EasySpeciesTree <SpeciesID prefix> <SingleCopyOrtho> <Orthogroups> <protein file> [thread] [bootstrap] [model]
Author: Wei Dong <1369852697@qq.com>, FAFU
Version: v1.0
Easily construct the ML species tree with all single-copy gene's protein sequences
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optional arguments:
-h, --help show this help message and exit
-in1 INPUT1, --input1 INPUT1
offer the prefix of all abbreviated species id
-in2 INPUT2, --input2 INPUT2
offer the Single-copy Orthogroups file, SingleCopyOrthogroups.txt
-in3 INPUT3, --input3 INPUT3
offer the all Orthogroups file, Orthogroups.csv
-in4 INPUT4, --input4 INPUT4
offer all species protein sequences
-t THREAD, --thread THREAD
set the number of thread, default=10
-nb BOOTSTRAP, --bootstrap BOOTSTRAP
set the number of bootstrap, default=100
-m MODEL, --model MODEL
set the model of amino acid substitution, default=PROTGAMMAJTT
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