User: kabir.deb0353

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Posts by kabir.deb0353

<prev • 37 results • page 1 of 4 • next >
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How to get genes with best Phylogenetic signal from multiple orthologous genes?
... Hello Experts, I have used BUSCO to get orthologous genes from 50 species. After that, I have sorted the 350 common orthologous genes from 50 species. Now I want to do phylogenetic analysis with the orthologous genes. But using concatenated 350 genes for phylogeny in MrBayes or RaxML is a very time ...
phylogeny simulation orthologous written 7 weeks ago by kabir.deb03530
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Answer: A: How to run beast.jar file using Slurm?
... SOLVED #!/bin/sh #SBATCH --job-name=R4_beast # Job name #SBATCH --ntasks=2 # Run on the no. of CPU #SBATCH --ntasks-per-node=2 # cores to spread across distinct nodes #SBATCH --output=R4_%j.log # Standard output log #SBAT ...
written 7 weeks ago by kabir.deb03530
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BEAST and BEAGLE installed using conda environment, how to connect?
... Hello experts, I have 2 version of BEAST, the BEAST v 1.10 is installed through conda environment, where BEAST v 2.6 have the binary file. Further I have installed BEAGLE v 5.1 using conda environment as I'm unable to install in formal manner at HPC as I don't have the permission. So, now how can ...
beauti beast written 8 weeks ago by kabir.deb03530
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How to run 2 programme one after another using single SLURM?
... Hello experts, I want to run 2 programme simultaneously using SLURM (serially) script by which output of 1st programme used as input of second programme. I have multiple fasta file as input, how can I do that! Thanks ...
slurm parallel written 8 weeks ago by kabir.deb03530 • updated 8 weeks ago by Mensur Dlakic3.4k
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Comment: C: How to remove internal stop codons from BUSCO identified orthologous genes?
... Hello, Actually I want to do phylogenetic analysis and substitution rate (ka/ks) calculation of orthologous gene set of a particular group of species (Gs). After sorting the common orthologous genes of Gs I implemented TranslatorX to align each orthologous genes. But TranslatorX result shows that ...
written 9 weeks ago by kabir.deb03530
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How to solve "String index out of Range" problem in macse.jar
... I'm trying to run [macse.jar][1] file in my sequence to replace internal stop codons from multifasta sequence using below command for i in *.fna do echo "${i}" java -jar macse.jar -prog exportAlignment -align "${i}" -ambi_OFF true -canonize_ON true -codonForFinalStop --- -codonFor ...
java sequence stopcodonremoval jar written 9 weeks ago by kabir.deb03530 • updated 10 days ago by Biostar ♦♦ 20
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How to remove internal stop codons from BUSCO identified orthologous genes?
... I have implemented BUSCO on few Genomes downloaded from NCBI, and I got multiple internal stop-codons in between the orthologous genes, how to remove or replace them with gaps. ...
busco stopcodon remove written 9 weeks ago by kabir.deb03530
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How to calculate rate of synonymous substitution at both 2 fold 4 fold degenerate sites
... Hello experts, I want to calculate the rate of synonymous substitution at both 2 fold 4 fold degenerate sites from multiple sequence alignment. How can I do it? Is there any software available for doing the same. Thanks ...
sequence evolution synonymous written 10 weeks ago by kabir.deb03530
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How to calculate rate of synonymous substitution at 4 fold and 2 fold degenerate sites?
... Hello experts, I was reading > 'Bierne, Nicolas, and Adam Eyre-Walker. "The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias." Genetics 165.3 (2003) ...
gene substitution paml written 10 weeks ago by kabir.deb03530 • updated 10 weeks ago by Pierre Lindenbaum126k
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Mutation Selection test FMutSel0-M0 (Null) FMutSel-M0 (Alternative) df=0, how to do Chi square test?
... Hello Experts, I am doing Mutation Selection test FMutSel0-M0 (Null) FMutSel-M0 (Alternative) of my test data set because of its AT richness, however, np for both models is coming same, 5. Therefore degrees of freedom become 0. In this scenario how can I do the Chi-square test. Some literature said ...
paml codeml written 10 weeks ago by kabir.deb03530 • updated 6 days ago by Biostar ♦♦ 20

Latest awards to kabir.deb0353

Scholar 7 weeks ago, created an answer that has been accepted. For A: How to run beast.jar file using Slurm?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For GC Content and GC Skew are not showing in BRIG image
Popular Question 3 months ago, created a question with more than 1,000 views. For GC Content and GC Skew are not showing in BRIG image
Popular Question 6 months ago, created a question with more than 1,000 views. For Embedding NCBI standalone Blast or SequenceServer in a Website
Popular Question 19 months ago, created a question with more than 1,000 views. For Embedding NCBI standalone Blast or SequenceServer in a Website
Popular Question 19 months ago, created a question with more than 1,000 views. For How to Install Augustus properly ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For splitting Multifasta File Into A *Smaller Multifasta File containing few sequence

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