User: david_emms

gravatar for david_emms
david_emms40
Reputation:
40
Status:
New User
Location:
Last seen:
2 months, 4 weeks ago
Joined:
2 years, 3 months ago
Email:
d*********@hotmail.com

Posts by david_emms

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
738
views
1
answers
Answer: A: Problem in running OrthoFinder
... Hi In case this is helpful to anyone else with the same problem: If you've got another version of makeblastdb that is getting used by the system instead of the one you want then just put the directory containing the one you want to use at the start of your PATH variable instead of at the end e.g. ...
written 3 months ago by david_emms40
0
votes
1
answer
276
views
1
answers
Answer: A: How to plot Orthofinder results?
... Hi Zhang There are really hundreds of ways to use the results from OrthoFinder to do all kinds of different analyses, that's the idea! You mention some gene family analyses, can you give some more information about what it is you'd like to investigate about the gene families or what it is you'd lik ...
written 3 months ago by david_emms40
0
votes
1
answer
679
views
1
answers
Answer: A: How can I extract paralogs and orthologs seperately from Orthofinder output?
... Hi In case anyone else has this question.... the current versions of OrthoFinder now produce files of orthologues between each species pair that it infers by analysing the gene trees. If you also want to specifically find paralogous genes then these are the genes in the Orthogroup.csv file that ar ...
written 5 months ago by david_emms40
1
vote
2
answers
898
views
2
answers
Answer: A: Phylogenetic tree based on orthofinder results
... Hi OrthoFinder produces a gene tree for each orthogroup, this means you get gene trees for all your genes in all your species. These trees show how each gene is related to its orthologues and recent paralogues (paralogues that diverged since the last common ancestor of your set of species). It als ...
written 6 months ago by david_emms40
0
votes
2
answers
548
views
2
answers
Answer: A: How can I update OrthoFinder
... Hi Just to say, you can download the latest version of OrthoFinder, untar it anywhere on your computer and just run it from there. You don't need put it in your bin directory, you can just run it by typing the path to the version you want to call. All the best David ...
written 6 months ago by david_emms40
0
votes
1
answer
588
views
1
answers
Comment: C: OrthoFinder running time
... Install DIAMOND on your machine and have it in the system path so that you can call it using "diamond". Then when calling orthofinder you just need to add the option "-S diamond_more_sensitive" for version 2.0.0 or earlier of just "-S diamond" in future versions. All the best David ...
written 7 months ago by david_emms40
1
vote
2
answers
275
views
2
answers
Answer: A: Will lowering the LengthTol parameter increase false positive links in Orthology
... Hi It's worth trying [OrthoFinder][1], it has a correction for gene length that addresses this exact problem (short genes getting excluded). If you run it using DIAMOND it's extremely fast so it'd be very easy to get results and compare them with OMA. All the best David [1]: https://genomebi ...
written 7 months ago by david_emms40
0
votes
1
answer
588
views
1
answers
Answer: A: OrthoFinder running time
... Hi OrthoFinder developer here! The very first thing to say is that I've recently added the option to use [DIAMOND][1] instead of BLAST and I'm really impressed with it. From now on I would recommend virtually always using DIAMOND with OrthoFinder as it's about **60x faster** in the tests I've done ...
written 7 months ago by david_emms40
2
votes
3
answers
759
views
3
answers
Answer: A: Finding orthologs of 100 human genes in 44 insect transcriptomes
... Hi Anuj I've just added a large amount of new functionality to [OrthoFinder][1] so it now infers orthologues as well as orthogroups. To do this it constructs orthogroups and then infers the gene tree for each orthogroup which is uses to identify orthologues (i.e. it does it the 'proper way' identif ...
written 20 months ago by david_emms40

Latest awards to david_emms

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1685 users visited in the last hour