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What file format is this?

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  • What file format is this?

    Hi everyone,
    I found this alignment in a format I don't recognize, neither my phylogenetic programs. Any idea? And any way to convert it to fasta, phylip, etc...
    Thanks
    Code:
    193 Ce 13A10 Z46934        -------------------------MTQSLAHKNAWQC--   13
    194 Ce 13A8 Z48717 T10B9.4 ----------------------------------------    0
    195 Ce 13A7 Z48717 T10B9.10-------------------------MSFSI----------    5
    196 Ce 13A6 Z48717 T10B9.3 -------------------------MIFVL----------    5
    197 Ce 13A5 Z48717 T10B9.2 -------------------------MSLSI----------    5
    198 Ce 13A4 Z48717 T10B9.1 -------------------------MSLSL----------    5
    199 Ce 13A3 Z48717 T10B9.5 -------------------------MSLSI----------    5
    200 Ce 13A2 Z48717 T10B9.7 -------------------------MSLGF----------    5
    201 Ce 13A1 Z48717 T10B9.8 -------------------------MGYF-----------    4
    202 Ce 25A1 Z66495 C36A4.1 -------------------------MAL------------    0
    203 Ce 25A2 Z66495 C36A4.2 -------------------------MAL------------    0
    204 Ce 25A3 Z66495 C36A4.3 -------------------------MAF------------    0
    205 Ce 25A4 Z66495 C36A4.6 -------------------------MAI------------    0
    206 Ce 14A1 Z50742 K09A11.2----------------------------------------    0
    207 Ce 14A2 Z50742 K09A11.3----------------------------------------    0
    208 Ce 14A3 Z50742 K09A11.4----------------------------------------    0
    209 Ce 14A4 Z50742 + R04D3 ----------------------------------------    0
    210 Ce 16A1 Z54269         ----------------------------------------    0
        Ce      U55365 C12D5.7 ----------------------------------------    0
        Ce      U50311 C25E10.2----------------------------------------    0
    211 Ce 22A1 U39648 T13C5.1 SSWIKCRDWMAFALSHHIIMGIYLLILRNFLPQVVPDFEW    0
    212 Ce 23A1 U39472 B0304.3 -------------MPIAYFLPSQVNSGVCCLICRHWYLIG    0

  • #2
    I suggest writing a PERL script to convert the data into the format you desire.
    The alignment file looks very similar to Phylip format. Maybe you can just load it into Excel and manually modify it to the desired format.

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    • #3
      Thanks for the suggestion. Yep, the only way to get something from it was parsing it along. It's like a pre-clustal aligment with extra headers (it is from mid-late 90's).

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