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# Running Orthologue Prediction
## 1. Checking required programs are installed
Test can run "fastme -i myfilepath/SimpleTest.phy -o myfilepath/SimpleTest.tre" - ok
Test can run "dlcpar_search --versi…
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Hello,
I may have missed it in the readme and the paper, but does Orthofinder do a distinction between inparalogs and outparalogs when building orthogroups ?
Thank you.
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David,
In Orthogroups.txt, when there is more than 1 member of a group, how is the order of the members determined?
```
OG0000382: contig1 contig2 contig3 contig4
```
Is contig1 the 'most …
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Hi David,
Can you explain a little bit about how orthofinder reconstruct species tree?
I did not give species tree as input. But it produced a SpeciesTree_rooted.txt file in Orthologoues folder.
…
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If, for whatever reason, fastme creates an empty tree file then OrthoFinder crashes when it tries open the file (as the newick tree reader throws an exception):
> Best outgroup(s) for species tree
…
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*\* Recursive MCL **
MCL runs processed: 9027. Sequences placed: 0/143. Run time: 2 days, 0 hrs, 29 min, 56 secTraceback (most recent call last):
File "./rdmcl.py", line 1037, in
logging.warnin…
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After posting I realized you're at ver. 1.1.4 so I'm getting it updated on our cluster and I'll see if that solves the problem. If not, I'll update again.
Hi David,
I think is may be a problem …
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Hi every one,
I'm wondering how OrthoFinder is bulding orthogroups ?
It looks like OrthoFinder is using a reference species (the last species in alphanumerical order ?) which is changing the numb…
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I was just loading cypher-shell and it ended up failing
```
$ cypher-shell
Connected to Neo4j 3.1.1 at bolt://localhost:7687 as user neo4j.
Type :help for a list of available commands or :exit …
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Hi guys,
First, thank you for the great tool.
I am looking at the Statistics_PerSpecies.csv file for a few of my runs. There are four tables (below). The second & fourth are percentages but what is …