User: DR

gravatar for DR
DR10
Reputation:
10
Status:
New User
Location:
European Union
Last seen:
2 weeks ago
Joined:
2 years, 5 months ago
Email:
d*********@gmail.com

Posts by DR

<prev • 6 results • page 1 of 1 • next >
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Best coverage measurements specifically for genes
... Hi everyone! I am working on a metagenomics project and I constructed a gene catalog for all the metagenomic samples. I want to identify the coverage for each of the genes in the catalog. So far, I tried Samtools depth and I used the average coverage per position in the gene as a coverage measure. ...
metagenomes coverage gene-catalog written 9 weeks ago by DR10
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Estimating dN/dS directly from BAM/SAM files
... Hello everybody! I am working with metagenome assemblies and I am making gene prediction on them. The next step I would like to carry out is to map my reads into those predicted genes and to estimate dN/dS based on these mapping files (BAM/SAM) Does someone know if there is any pre-existing tool pe ...
assembly gene prediction dn/ds bam/sam written 12 months ago by DR10
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Running PAML models on HyPhy
... Hi! I've been running several site models on PAML but now I would like to perform the same analyses on HyPhy. I don't know exactly how can I specify to launch the M7 and M8 models from PAML on Hyphy. I tried to use the NielsenYang.bf batch file and I could see that the 16th model under a GY94 subst ...
hyphy phylogenetics paml site models written 2.4 years ago by DR10 • updated 2.4 years ago by SES7.9k
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Answer: A: branch model analysis codeml
... Thanks! I used NJ for the topology reconstruction. Do you know if I need to test the molecular clock, or should I just assume clock=0? ...
written 2.5 years ago by DR10
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branch model analysis codeml
... Hi! I'm trying to observe positive selection events before gene duplication, so I'm performing  a branch model analysis. I was wondering if it's essential to incorporate an outgroup. If it's, do you know how divergent should be this outgroup? Thanks a lot! ...
paml codeml written 2.5 years ago by DR10
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How can the node distances affect to the omega values on the site model performed by codeml?
... Hi! I'm performing a site positive selection test with codeml. I used the p-distance for obtaining the tree topology that then I used in order to contrast the different models for detecting positive selection. In spite of obtaining the same tree typology, could you give me an idea about how can the ...
phylogeny paml codeml written 2.5 years ago by DR10 • updated 2.5 years ago by Brice Sarver2.3k

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