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Commits on Oct 22, 2024

• Update README.md

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Commits on Oct 20, 2024

• Report error if species tree inference fails, resolves #919

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Commits on Oct 7, 2024

• Update for python 3.11

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• Label Beta release

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• Add '--assign' example to README

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• Add Additional Species to Example Data

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• Merge v3: linear_species_addition

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• Don't delete m matrix

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• Update requirements

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Commits on Mar 1, 2024

• Name OG/HOG profiles

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Commits on Feb 29, 2024

• Handle HOGs/OGs as base for profiles

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Commits on Feb 27, 2024

• Correct assigning of genes to HOGs

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Commits on Feb 9, 2024

• Correct queues

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Commits on Jun 1, 2023

• Ortholog writing parallelisation

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Commits on May 31, 2023

• Don't delete m matrix

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Commits on May 17, 2023

• Add --assign notes to REDME

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Commits on May 15, 2023

• Update version number

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• Only check blast for dendroblast. iOGs4

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Commits on May 12, 2023

• Write stats for phylogenetic OGs

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• Reduce default inflation

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• Only-groups workflow for fast-add

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Commits on May 4, 2023

• Check for fast-add dependencies

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Commits on Apr 29, 2023

• Write & read N0.ids.tsv

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Commits on Apr 28, 2023

• Tidy terminal output

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Commits on Apr 27, 2023

• Split diamond searches to reduce RAM

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Commits on Apr 24, 2023

• Fix cmd formatting

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Commits on Apr 22, 2023

• SHOOT.bio homology clusters

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• Some method calls via PTM

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• Use multithreading for launch external processes

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Commits on Apr 19, 2023

• Cluster between-core clades one-by-one

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Commits on Apr 17, 2023

• Reduce profile size, capture diamond error

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Commits on Mar 30, 2023

• Fix alignment of tree/msa files

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• Infer remaining MSA

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Commits on Mar 29, 2023

• Fix clade-specific OGs, handle iogs4

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Commits on Mar 28, 2023

• WIP Workflow with species tree inference

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