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Questions tagged [megax]

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Converting .tsv to .meg for visualization

This is an add-on to the previous question I asked here. I was able to deploy a "chunking" strategy to my kmer matrix and was able to get a file with the distance measurements! From what I ...
rimo's user avatar
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0 votes
1 answer
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Aligning sequences with multiple genetic codes!

I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding ...
George X.'s user avatar
2 votes
1 answer
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MEGA11 gives the error "stop codons are found in the translated sequences", even though there are not!

I am using MEGA11 MEGA11: Molecular Evolutionary Genetics Analysis Version 11 , Mol. Biol. Evol. 38(7):3022–3027 to align protein coding sequences that I downloaded from KEGG database. I am ...
George X.'s user avatar
2 votes
2 answers
418 views

Convert Symmetrix Matrix into Lower Triangular Matrix

I'm using Scipy's pdist function to calculate a distance matrix which is working great but it gives me a symmetric matrix and I want to convert it into a lower-left triangular matrix. This is what it ...
rimo's user avatar
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1 vote
1 answer
80 views

MegaX Pairwise Matrix Error

I have a pairwise matrix that I've manually formatted into a ".mega" file following the guide in the MegaX documentation but when I go to import it into the application it gives this error: <...
rimo's user avatar
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