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  • would like to convert aln to axt for Ka Ks calculator

    Hello, everyone,

    I would like to ask how to convert fasta file or .aln to .axt for ka ks calculation.

    I have the .aln file now and have to convert it to .axt, and I have a huge amount of data so that I cannot do it one by one. Is there any python or perl script can do this? Otherwise how could you deal with large sets of data for ka ks calculation?

    To make it much more clearer,
    the original .aln file is like this:
    AM_Ensembl001_A1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    DT_Ensembl001_A1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    UW_Ensembl001_A1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC


    AM_Ensembl001_A1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    DT_Ensembl001_A1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    UW_Ensembl001_A1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC


    AM_Ensembl002_A2 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
    DT_Ensembl002_A2 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
    UW_Ensembl002_A2 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF


    AM_Ensembl002_A2 DDDDDDDD
    DT_Ensembl002_A2 EE
    UW_Ensembl002_A2 FFFFF


    And I would like to convert it like this:

    Ensembl001
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

    CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

    Ensembl002

    DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD

    EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF


    Looking forward to your reply!

    All the best,

    Sadiexiaoyu
    Last edited by sadiexiaoyu; 01-25-2017, 06:07 PM. Reason: make the question much more clearer

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