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Old 07-14-2013, 07:18 PM   #1
Shorash
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Default KaKs calculator help (merging fasta files)

Hi guys,

I'm trying to merge and align 2 fasta files to get them into quasi-axt format for kaks calculations. The two fasta files are very large ~6 gigabases each. I'm not sure what program allows me to combine and align the two. Any help would be appreciated, here's a link to the example provided by the calculator.

https://code.google.com/p/kaks-calculator/wiki/AXT
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Old 07-15-2013, 06:42 PM   #2
Shorash
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anyone used it before?
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Old 07-15-2013, 06:55 PM   #3
GenoMax
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Are these multiple fasta files or just 2 large fasta files with single sequence in each?

I wonder if you can use the LASTZ aligner to get the AXT format files: http://www.bx.psu.edu/~rsharris/lastz/
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Old 07-16-2013, 07:09 PM   #4
Shorash
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Quote:
Originally Posted by GenoMax View Post
Are these multiple fasta files or just 2 large fasta files with single sequence in each?

I wonder if you can use the LASTZ aligner to get the AXT format files: http://www.bx.psu.edu/~rsharris/lastz/
I have two separate large fasta files for two species that I wish to use in the kaks calculator. Each file contains assembled pair end reads for the respective species.
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Old 07-28-2013, 09:19 AM   #5
k-gun12
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You won't be able to just align nucleotide contigs and run the KaKs calculator.. it needs a codon alignment as input.. i.e properly aligned CDS sequence with no UTR and/or indels. A single indel will destroy the alignment. I usually use a combination of estwise and translatorx.
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