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How to prep MAFFT alignment files for use in R packages ape and pegas?

R pegas alignment population genetics written 11 days ago by juliuspasion1994 • 10

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603

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Formatting Haplotype Network in R

R pegas haplotypenetwork written 9 months ago by christinafragel • 0 • updated 7 months ago by zx8754 ♦ 8.2k

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Identifying mutations between haplotypes using haploNet (pegas) in R

haplotypes R pegas phylogenetics written 18 months ago by GabrielMontenegro • 530 • updated 15 months ago by Jie Ping • 20

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2.6k

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Pegas import fasta and calculate theta

fasta R pegas theta written 4.7 years ago by Adrian Pelin • 2.3k • updated 4.7 years ago by David W ♦ 4.7k

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Recent Replies

C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab by bhanu.chandra1 • 10
Thank you Ram :). I will take it as a learning experience.
C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab by RamRS ♦ 24k
Please use the formatting bar (especially the `code` option) to present your post better. You can...
C: Counting number of hits of blastn output by caranlove • 0
Thank you for the insight! This is helpful, but I am actually most interested in how many of the ...
C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab by bhanu.chandra1 • 10
# set the base colour as 'black' keyvals <- rep('#000000', nrow(res_A_W_lfc)) ...
C: Counting number of hits of blastn output by Giovanni.madrigal12 • 100
Adding to this comment, cut -f1 | sort | uniq -c This will give you the number of hits eac...
A: Counting number of hits of blastn output by lieven.sterck ♦ 5.9k
At first sight (but I assume it might be simply a typo) this command will not work as the `-out` ...
C: Maker2 Transcriptome Input by Juke-34 • 2.7k
I checked on the MAKER mailing list lt lools like `altest` creates hints for ab initio gene predi...
A: Plenty of gaps with my sam alignment file, why is that? by WouterDeCoster ♦ 41k
I don't see any real gaps. What I can see are small false indels, which is the dominant error pat...
C: centrifuge not working- index error by genomax ♦ 71k
Using `+` in unix names is likely not a good idea. Try renaming the files (you may need to recrea...
C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab by Kevin Blighe ♦ 48k
Hey, which code are you running, exactly?
C: How to convert log2FC (Fold Change) obtained by differential expression analysis by patrickhoey23 • 0
Hi ZheFrench, Is there a reference I can get for this or is that a nonsensical question?
C: Generating consensus sequence from bam file by jkbonfield • 180
"samtools mpileup foo.bam" will produce the columns showing what bases are aligned at each positi...

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