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halTreePhyloP.py failed w/ unclear error

Status: Open.

#331 In ComparativeGenomicsToolkit/hal;

· brantfaircloth opened on Apr 13, 2026

Make halPhyloPTrain.py run in multithreaded mode (w/ PhyloFit)

Status: Open.

#329 In ComparativeGenomicsToolkit/hal;

· brantfaircloth opened on Apr 1, 2026

halPhyloPTrain.py fails with hal2mafMP.py error

Status: Open.

#328 In ComparativeGenomicsToolkit/hal;

· brantfaircloth opened on Mar 20, 2026

Rename .hal file species

Status: Open.

#318 In ComparativeGenomicsToolkit/hal;

· msGreen98 opened on Feb 6, 2025

hal2assemblyhub.py: A Toil workflow can only be started once. Use Toil.restart() to resume it.

Status: Open.

#317 In ComparativeGenomicsToolkit/hal;

· twooldridge opened on Feb 3, 2025

Compile in remote HAL access by default

Status: Open.

#310 In ComparativeGenomicsToolkit/hal;

· diekhans opened on Nov 23, 2024

Build Error with HAL Using HDF5

Status: Open.

#309 In ComparativeGenomicsToolkit/hal;

· liangminliu opened on Oct 30, 2024

GapDeletion

Status: Open.

#308 In ComparativeGenomicsToolkit/hal;

· shuiyanwu778 opened on Oct 11, 2024

Unclear conversion extraction subsetting

Status: Open.

#307 In ComparativeGenomicsToolkit/hal;

· fgualdr opened on Oct 7, 2024

masking sites in target genome after alignment

Status: Open.

#303 In ComparativeGenomicsToolkit/hal;

· JeffWeinell opened on Jun 4, 2024

A question about halLiftover

Status: Open.

#301 In ComparativeGenomicsToolkit/hal;

· Marh32 opened on Apr 25, 2024

Error when running halLiftover

Status: Open.

#300 In ComparativeGenomicsToolkit/hal;

· zwymic00 opened on Apr 25, 2024