5 Homology Inference

5.1 Core

Command

genetribe core -h

# Tool:  GeneTribe core
# Usage: genetribe core -l <FirstName> -f <SecondName> [options]
# 
# Description:
#   Core workflow of GeneTribe
# 
# Options:
#   -h         Show this message and exit
#   -l <str>   Prefix name of first file
#   -f <str>   Prefix name of second file
#   -d <dir>   Pre-computed BLAST file in <dir> [default ./]
#   -r         Calculate chromosome group score [default True]
#   -c         Calculate confidence score [default False]
#   -s <str>   The string for spliting gene from transcript ID [default .]
#   -e         E-value of BLASTP [default 1e-5]
#   -n <int>   Number of threads for blast [default 36]
#   -b <float> Threshold based on BSR for filtering Match Score(0-100) [default 75]
# 
# Author: Chen,Yongming; chen_yongming@126.com

Parameters

Table 3. Parameters in genetribe core
Parameter Description Default Required
-h Print brief help message
-l The prefix name of the files of genome 1, such as prefix_name.bed, prefix_name.fa, prefix_name.chrlist and prefix_name.confidence yes
-f The prefix name of the files of genome 2, such as prefix_name.bed, prefix_name.fa, prefix_name.chrlist and prefix_name.confidence yes
-d If you have any of the pre-computed files, including name1_name2.blast, name2_name1.blast, name1_name1.blast and name2_name2.blast, put it in directory "dir" and add the parameter "-d dir" to genetribe core, the program will skip BLAST step ./
-r Whether to add penalty ratio to the match score according to subgenome group True
-c Whether to add penalty ratio to the match score according to gene annotation confidence False
-s The separator is used to distinguish gene ID from transcript ID (for more detail, see File formats) .
-e The e-value in BLASTP. In general, the lower the threshold, the fewer results you get 1e-5
-n Number of threads. BLASTP will be calculated in parallel, so the number of threads will be divided equally 1
-b Filtering threshold. The final filtering threshold is 'BSR × Filtering threshold × α' 75

5.2 sameassembly

command

genetribe sameassembly -h

# Tool:  GeneTribe sameassembly
# Usage: genetribe sameassembly -l <firstname> -f <secondname> [options]
# 
# Description:
#   Homology inference for the same assembly
# 
# Options:
#   -h Show this message and exit
#   -l <string> Prefix name of first assembly
#   -f <string> Prefix name of second assembly
# 
# Author: Chen,Yongming; chen_yongming@126.com

Parameters

Table 4. Parameters in genetribe sameassembly
Parameter Description Required
-h Print brief help message
-l The prefix name of the files of genome 1, such as prefix_name.bed and prefix_name.genelength yes
-f The prefix name of the files of genome 2, such as prefix_name.bed and prefix_name.genelength yes