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alignproteome added#875

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martin-steinegger wants to merge 33 commits intosoedinglab:mastersoedinglab/MMseqs2:masterfrom Gyuuul2:masterGyuuul2/MMseqs2:masterCopy head branch name to clipboard

+918-23

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Commits on Aug 16, 2024

• alignproteome added

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Commits on Aug 19, 2024

• add workflow, revise based on feedback

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Commits on Aug 25, 2024

• Change createdb.cpp so that it takes in ".txt" file containing paths of different fasta files

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• Merge remote-tracking branch 'refs/remotes/origin/master'

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Commits on Aug 26, 2024

• Change filepath format from txt to tsv. Also add explanations of its usage to createdb and easy-search in MMseqsBase.cpp.

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Commits on Aug 27, 2024

• createtsv - handle source identifier

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• proteomcluster - change writer / way to select repProteome

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• easy proteomecluster workflow

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• indexreader - handle source identifier

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• update mmseqsbase and change module name into proteomecluster

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Commits on Aug 28, 2024

• set alignment mode default

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• latest

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• original index

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• use sync_fetch_and_add when increment memcount

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• change submat

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• add timer

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• Merge branch 'pr-879'

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• Remove __packed__ to resolve sync_fetch_and_add error

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Commits on Aug 29, 2024

• change chmod in createdb

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• update proteome-similarity threshold parameter

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Commits on Sep 9, 2024

• Sort redundant proteomes by similarity score in proteome_cluster.tsv

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• delete redundant code - checking proteome is singleton(no redudant member proteome is detected)

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• stop

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• jaccardindexTrial

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• add normalized scoring

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• add proteome relative(normalized) similarity threshold parameter

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• relative similarity threshold

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• latest version-bugfix,relativeProteomeSimilarity added, singleton proteome handling update

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Commits on Sep 10, 2024

• Change Relative Score formula

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• Remove Debug printout

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• style change

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• Latest Version

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Commits on Sep 19, 2024

• Add cluster count report

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