[Inparanoid] Inparanoid 4.1 standalone output

Steffen Priebe steffen.priebe at hki-jena.de
Wed Feb 11 13:37:30 CET 2015

I applied the inparanoid standalone version 4.1 to find homologs between 
two species
using 2 protein FASTA files. Inparanoid generated the following output 


The HTML file and the Output.* file both list the number of orthologe 
groups found,
as well as the number of in-paralogs in each species:

9888 groups of orthologs
12352 in-paralogs from species1.fasta
11012 in-paralogs from species2.fasta

Anyhow, the Output.* file additionally outputs the following numbers (in 
the first 4 lines):
23603 sequences in file species1.fasta
20208 sequences in file species2.fasta
20845 sequences species1.fasta have homologs in dataset species2.fasta
17870 sequences species2.fasta have homologs in dataset species1.fasta

I was wondering where to find these genes listed in line 3+4, which are 
larger compared to the number of in-paralogs?
In the 4 output files (orthology.*.html, Output.*, table.*, sql.*) only 
the 9888 groups including the 12352 and 11012 genes are listed.

It also not clear to me how to output in the last 3 files is organised 
and what each column means:
Example of the first 3 rows:
gene1.species1    gene1.species2    184.1    110    541    92 92    
92    92    q:1-92 h:439-530
gene1.species1    gene2.species2    181.0    110    539    97 97    
97    97    q:1-97 h:440-536
gene1.species1    gene3.species2    50.1    110    211    81 82    81    
82    q:1-81 h:123-204

There was no description for these kind of output.

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