From steffen.priebe at hki-jena.de  Wed Feb 11 13:37:30 2015
From: steffen.priebe at hki-jena.de (Steffen Priebe)
Date: Wed, 11 Feb 2015 13:37:30 +0100
Subject: [Inparanoid] Inparanoid 4.1 standalone output
Message-ID: <54DB4D0A.4010602@hki-jena.de>

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

orthologs.species1.fasta-species2.fasta.html
Output.species1.fasta-species2.fasta
table.species1.fasta-species2.fasta
sql.species1.fasta-species2.fasta
species1.fasta-species2.fasta
species1.fasta-species1.fasta
species2.fasta-species2.fasta

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.

From apelin20 at gmail.com  Thu Feb 19 19:57:11 2015
From: apelin20 at gmail.com (Adrian Pelin)
Date: Thu, 19 Feb 2015 13:57:11 -0500
Subject: [Inparanoid] Slow Analysis
Message-ID: <54E63207.9000103@gmail.com>

Hello,

I noticed inparanoid has not been updated to work with the new 
NCBI-Blast and still uses legacy blast. I was wondering if there was a 
way to tweak the code to use the new blast, since it's much faster. I am 
trying to find orthologues between a fish species and zebrafish, and 
it's been on the first step for a few days now where it blasts zebrafish 
against zebrafish.

Thanks,
Adrian