Orthologous groupsCAZyme domain sequences
正交群体采用CAZyme域序列来运行OrthoMCL程序（http://orthomcl.org/orthomcl/）。这是通过多个步骤完成的，每个步骤如下所述：
1.域FASTA序列根据其家族被分类到文件中。
2.每个FASTA系列文件都使用程序makeblastdb进行了一些BLAST数据库的默认设置。
3.对于每个家族，FASTA文件使用具有默认设置的blastp对同名数据库进行运行，所有输出均为表格。
4.为每个家族运行orthomclAdjustFasta，以家族为标识。
- orthomclBlastParser是使用步骤3的BLAST结果和从步骤4创建的兼容的fasta文件运行的。
6.正在运行orthomclInstallSchema，使用默认配置文件，但数据库的登录信息除外。
7.运行orthomclLoadBlast，使用步骤5中生成的文件。
8.orthomclPairs使用清理运行。
9.运行orthomclDumpPairs。
10.运行mcl mclInput，使用--abc和-I 1.5。
11.使用从步骤3生成的文件运行orthomclMclToGroups，并从第10步输入文件。
12.得到的文件给出每个直向同源组在一个单独的行。
Orthologous groupsCAZyme domain sequences were taken to run OrthoMCL program (http://orthomcl.org/orthomcl/
). This was done in a number of steps, each of which is explained below: - The domain FASTA sequences were sorted into files based on their family.
- Each family FASTA file was profiled into a BLAST database using the program makeblastdb with default settings.
- For each family, the FASTA file was run against the database of the same name using blastp with default settings, with all output being tabular.
- orthomclAdjustFasta was run for each family, using the family as the identifier.
- orthomclBlastParser was run using the BLAST results from step 3, and the compliant fasta file created from step 4.
- orthomclInstallSchema was run, the default configuration file was used, except for the login information to the database.
- orthomclLoadBlast was run, using the file generated in step 5.
- orthomclPairs was run with cleanup.
- orthomclDumpPairs was run.
- mcl mclInput was run, using --abc and -I 1.5.
- orthomclMclToGroups was run using the file generated from step 3, and inputing the file from step 10.
- The resulting file gives each orthologous group on a separate line.
