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205

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Use of OrthoFinder pipeline

species tree ortholog prediction phylogenomics written 9 months ago by basusudipto92 • 0

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2.9k

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map gene gain loss on species tree

reconciliation species tree gene tree written 5.3 years ago by Anand Rao • 350 • updated 10 months ago by xmuraji • 0

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666

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Building gene trees

bucky species tree astral gene tree written 16 months ago by Colaptes • 40 • updated 16 months ago by Brice Sarver • 3.6k

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317

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STRAW & MP-EST tree

species tree gene tree written 16 months ago by najmehparvaz • 0

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627

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Clarification of OMA tree metrics

orthologs oma species tree written 2.1 years ago by samche42 • 0 • updated 17 months ago by Biostar ♦♦ 20

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746

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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 2.1 years ago by samche42 • 0

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Recent Replies

C: Getting alignments with lower scores on Biopython by Mensur Dlakic • 8.1k
Yes. Beware that most of them will be completely meaningless. For example, you can create an alig...
C: map subsetByOverlaps back to input coordinates by brtawe • 0
That works great, thanks for the help!
C: Design Matrix with EdgeR or DESeq2 by rpolicastro ♦ 3.1k
Your design matrix will depend on what questions you are trying to answer and the presence of con...
C: Design Matrix with EdgeR or DESeq2 by i.sudbery ♦ 10k
You are likely to get a better reply to this on bioconductor.
A: Design Matrix with EdgeR or DESeq2 by i.sudbery ♦ 10k
You can't directly compare treated to untreated while taking `time` and `dose` into account with...
C: Pairwise2 Alignment Gap Penalties by Mark • 850
You can define a callback gap function for such cases then: c A callback function return...
A: map subsetByOverlaps back to input coordinates by rpolicastro ♦ 3.1k
Example data. library("GenomicFeatures") my_coords <- structure(list(seqnames = stru...
C: Design Matrix with EdgeR or DESeq2 by Kevin Blighe ♦ 69k
Cross-posted: https://support.bioconductor.org/p/p134163/
C: trimming of fasta file by Mark • 850
I disagree! Sometimes it's easier to just use a gui and get the job done. This is a good example ...
C: trimming of fasta file by Pierre Lindenbaum ♦ 133k
https://thomas-cokelaer.info/blog/2011/05/awk-the-substr-command-to-select-a-substring/
C: trimming of fasta file by harry • 10
Can you please tell me how is it I doing this because I want a 150 bp sequence from the middle? ...
C: RNA-Seq, HTSeq-Counts, counts are ~1M less compared to the reference research pa by GenoMax ♦ 94k
Most NGS aligners are non-deterministic i.e. you may not get exactly identical alignments if you ...

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