Issues

• halTreePhyloP.py failed w/ unclear error

  ComparativeGenomicsToolkit/hal#331 · Filter by author brantfaircloth opened on Apr 13, 2026
  3

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

  ComparativeGenomicsToolkit/hal#329 · Filter by author brantfaircloth opened on Apr 1, 2026
  2

• halPhyloPTrain.py fails with hal2mafMP.py error

  ComparativeGenomicsToolkit/hal#328 · Filter by author brantfaircloth opened on Mar 20, 2026

• Rename .hal file species

  ComparativeGenomicsToolkit/hal#318 · Filter by author msGreen98 opened on Feb 6, 2025
  2

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

  ComparativeGenomicsToolkit/hal#317 · Filter by author twooldridge opened on Feb 3, 2025
  1

• Compile in remote HAL access by default

  ComparativeGenomicsToolkit/hal#310 · Filter by author diekhans opened on Nov 23, 2024
  1

  

• Build Error with HAL Using HDF5

  ComparativeGenomicsToolkit/hal#309 · Filter by author liangminliu opened on Oct 30, 2024
  5

• GapDeletion

  ComparativeGenomicsToolkit/hal#308 · Filter by author shuiyanwu778 opened on Oct 11, 2024
  1

• Unclear conversion extraction subsetting

  ComparativeGenomicsToolkit/hal#307 · Filter by author fgualdr opened on Oct 7, 2024
  1

• masking sites in target genome after alignment

  ComparativeGenomicsToolkit/hal#303 · Filter by author JeffWeinell opened on Jun 4, 2024
  2

• A question about halLiftover

  ComparativeGenomicsToolkit/hal#301 · Filter by author Marh32 opened on Apr 25, 2024
  5

• Error when running halLiftover

  ComparativeGenomicsToolkit/hal#300 · Filter by author zwymic00 opened on Apr 25, 2024
  2

• Error processing SEQNAME_ARRAY with h5py

  ComparativeGenomicsToolkit/hal#295 · Filter by author bjeight opened on Feb 15, 2024
  1

• hal2assemblyhub fails when lifting over --bedDirs

  ComparativeGenomicsToolkit/hal#291 · Filter by author brantfaircloth opened on Jan 17, 2024

• Can deletedgenomes or subtree be recovered?

  ComparativeGenomicsToolkit/hal#289 · Filter by author Baohua-Chen opened on Jan 4, 2024
  2

• hal2maf into vcf

  ComparativeGenomicsToolkit/hal#285 · Filter by author tzaquin opened on Oct 23, 2023
  3

• Small issue with halWriteNucleotides (?fix described)

  ComparativeGenomicsToolkit/hal#283 · Filter by author lukebharrison opened on Oct 12, 2023

• halAlignmentDepth with SNPs

  ComparativeGenomicsToolkit/hal#282 · Filter by author hy09 opened on Sep 28, 2023

• cactus-hal2maf Error

  ComparativeGenomicsToolkit/hal#281 · Filter by author shuifeng1988 opened on Sep 24, 2023
  2

• Extracting Gene Annotations

  ComparativeGenomicsToolkit/hal#278 · Filter by author tli824 opened on Jul 19, 2023
  1

• cactus-hal2maf generates incomplete maf result

  ComparativeGenomicsToolkit/hal#277 · Filter by author xiaoyezao opened on Jun 29, 2023
  6

• Help with halPhyloPTrain.py

  ComparativeGenomicsToolkit/hal#274 · Filter by author xiaoyezao opened on Jun 15, 2023
  7

• Detecting synteny among multiple genomes?

  ComparativeGenomicsToolkit/hal#272 · Filter by author aminakur opened on May 18, 2023
  5

• Filter species in a hal file

  ComparativeGenomicsToolkit/hal#271 · Filter by author agduncan94 opened on May 4, 2023
  2

• halSnps - extract snps and corresponding coordinates across targetGenomes

  ComparativeGenomicsToolkit/hal#269 · Filter by author nicolo-tellini opened on Mar 31, 2023
  1