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alignproteome added #875

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alignproteome added #875

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Commits on Aug 16, 2024

  1. alignproteome added

    @Gyuuul2
    Gyuuul2 committed Aug 16, 2024
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Commits on Aug 19, 2024

  1. add workflow, revise based on feedback

    @Gyuuul2
    Gyuuul2 committed Aug 19, 2024
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Commits on Aug 25, 2024

  1. Change createdb.cpp so that it takes in ".txt" file containing paths … 

    …of different fasta files
    @elpis51613
    elpis51613 committed Aug 25, 2024
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  2. Merge remote-tracking branch 'refs/remotes/origin/master'

    @elpis51613
    elpis51613 committed Aug 25, 2024
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Commits on Aug 26, 2024

  1. Change filepath format from txt to tsv. Also add explanations of its … 

    …usage to createdb and easy-search in MMseqsBase.cpp.
    @elpis51613
    elpis51613 committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. createtsv - handle source identifier

    @Gyuuul2
    Gyuuul2 committed Aug 27, 2024
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  2. proteomcluster - change writer / way to select repProteome

    @Gyuuul2
    Gyuuul2 committed Aug 27, 2024
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  3. easy proteomecluster workflow

    @Gyuuul2
    Gyuuul2 committed Aug 27, 2024
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  4. indexreader - handle source identifier

    @Gyuuul2
    Gyuuul2 committed Aug 27, 2024
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  5. update mmseqsbase and change module name into proteomecluster

    @Gyuuul2
    Gyuuul2 committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. set alignment mode default

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  2. latest

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  3. original index

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  4. use sync_fetch_and_add when increment memcount

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  5. change submat

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  6. add timer

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  7. Merge branch 'pr-879'

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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  8. Remove __packed__ to resolve sync_fetch_and_add error

    @Gyuuul2
    Gyuuul2 committed Aug 28, 2024
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Commits on Aug 29, 2024

  1. change chmod in createdb

    @Gyuuul2
    Gyuuul2 committed Aug 29, 2024
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  2. update proteome-similarity threshold parameter

    @Gyuuul2
    Gyuuul2 committed Aug 29, 2024
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Commits on Sep 9, 2024

  1. Sort redundant proteomes by similarity score in proteome_cluster.tsv

    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  2. delete redundant code - checking proteome is singleton(no redudant me… 

    …mber proteome is detected)
    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  3. stop

    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  4. jaccardindexTrial

    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  5. add normalized scoring

    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  6. add proteome relative(normalized) similarity threshold parameter

    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  7. relative similarity threshold

    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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  8. latest version-bugfix,relativeProteomeSimilarity added, singleton pro… 

    …teome handling update
    @Gyuuul2
    Gyuuul2 committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. Change Relative Score formula

    @Gyuuul2
    Gyuuul2 committed Sep 10, 2024
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  2. Remove Debug printout

    @Gyuuul2
    Gyuuul2 committed Sep 10, 2024
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  3. style change

    @Gyuuul2
    Gyuuul2 committed Sep 10, 2024
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  4. Latest Version

    @Gyuuul2
    Gyuuul2 committed Sep 10, 2024
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Commits on Sep 19, 2024

  1. Add cluster count report

    @Gyuuul2
    Gyuuul2 committed Sep 19, 2024
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