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Showing: species tree • reset

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Building gene trees

bucky species tree astral gene tree written 8 weeks ago by Colaptes • 40 • updated 8 weeks ago by Brice Sarver • 3.2k

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134

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STRAW & MP-EST tree

species tree gene tree written 10 weeks ago by najmehparvaz • 0

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308

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Clarification of OMA tree metrics

orthologs oma species tree written 11 months ago by samche42 • 0 • updated 3 months ago by Biostar ♦♦ 20

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371

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R: apex Multigene alignment problems "DNA sequences in list not of the same length"

apex R astral species tree multigene alignment written 11 months ago by samche42 • 0

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2.3k

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map gene gain loss on species tree

reconciliation species tree gene tree written 4.1 years ago by Anand Rao • 250

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Recent Replies

A: any tool or R package for integrated analysis of miRNA and mRNA expression data by kristoffer.vittingseerup • 2.6k
There seems to be 12 R packages for miRNA analysis annotated in [Bioconductor][1] - maybe one of ...
C: any tool or R package for integrated analysis of miRNA and mRNA expression data by kristoffer.vittingseerup • 2.6k
Btw is the miranda database still maintained (or even available?). Alternatively there are other ...
C: any tool or R package for integrated analysis of miRNA and mRNA expression data by kristoffer.vittingseerup • 2.6k
Nice idea! To model the interactions more dicretly (trying to remove indirect effects) do you kno...
A: SAM flags needed for paired-end strand-specific differential expression by kristoffer.vittingseerup • 2.6k
I agree with @Amar - there is no need for requiring the paired end information but standness is i...
A: decreased genotyping rate after the conversion of lgen to ped and map by mingchen720 • 0
issue 1 was resolved after zeroing all female Y SNPs. But, still low call rate
C: Wrong feature labels when using BRIG tool by Joe ♦ 14k
Have you read the features in from the GBK in to the feature window?
C: conversion of .txt file to .bed by Joe ♦ 14k
`mv file.txt file.bed` *this highly advanced command should only be used if you know what you'...
C: Filter unique SNPs (rows) in VCF/text file by zx8754 ♦ 8.4k
Maybe `sort -u input.txt > output.txt` ?
C: Why is the number of genes in certain a module in WGCNA super high? by Arindam Ghosh • 200
I see I have similar situation in my analysis as well. The turquoise module has ~10000 of the 20k...
C: is there a web-based tool to cross-species compare multiple nucleotide or protei by Jean-Karim Heriche ♦ 21k
There's also the [Ensembl BLAST/BLAT page][1]. It defaults to human but you can add/remove specie...
C: UpSet R plot using text files by Jean-Karim Heriche ♦ 21k
The answer is: read the docs. If the issue can't be solved by this then you need to be more preci...
C: region amplified by primers designed for bisulfite by rezaee.genetic • 0
for example in an article the promoter of oct4 gene has been studied for methylation through bisu...

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