Issues

• phyluce_probe_slice_sequence_from_genomes raises KeyError with --flank due to str/bytes TwoBit key mismatch in v1.7.0

  faircloth-lab/phyluce#383 · Filter by author shangshanzhizhe opened on May 25, 2026

• phyluce_probe_run_multiple_lastzs_sqlite fails on genome names with dots or hyphens

  Enhancement
  faircloth-lab/phyluce#380 · Filter by author fdchevalier opened on Apr 10, 2026
  1

• phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed FileNotFoundError

  faircloth-lab/phyluce#379 · Filter by author eeeaston opened on Mar 8, 2026
  11

• error in matching contigs to barcodes

  faircloth-lab/phyluce#378 · Filter by author kostasandriotis07 opened on Nov 21, 2025
  1

• Adding unaligned.fasta files from new taxa to existing dataset

  faircloth-lab/phyluce#377 · Filter by author hutumpyancha opened on Sep 2, 2025

• Processing demultiplexed UCE fastq files from NCBI SRA

  faircloth-lab/phyluce#376 · Filter by author SaunakP25 opened on Aug 28, 2025
  5

• Error in Workflows Mapping

  faircloth-lab/phyluce#375 · Filter by author thu-115 opened on Aug 18, 2025

• phyluce_align_get_only_loci_with_min_taxa not giving the correct number of taxa in output

  faircloth-lab/phyluce#373 · Filter by author GabrielaFJacintho opened on Jun 4, 2025

• Too much information for Phyluce / SPAdes?

  faircloth-lab/phyluce#372 · Filter by author jb23590 opened on May 22, 2025
  7

• AttributeError: 'str' object has no attribute 'decode'. Did you mean: 'encode'?

  faircloth-lab/phyluce#371 · Filter by author mooreld opened on Apr 1, 2025
  2

• phyluce_assembly_get_fastas_from_match_counts

  faircloth-lab/phyluce#370 · Filter by author mlovelynn opened on Mar 27, 2025
  1

• How to handle long branches (fresh and degraded samples) and low UCE capture

  faircloth-lab/phyluce#367 · Filter by author jbernst opened on Feb 19, 2025
  2

• Issue with RAM

  faircloth-lab/phyluce#366 · Filter by author jb23590 opened on Feb 6, 2025
  4

• assembly_assemblo_spades: how to including several singletons fastq files?

  faircloth-lab/phyluce#363 · Filter by author Angelica-Pulido opened on Jan 17, 2025
  4

• Error running phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db

  faircloth-lab/phyluce#362 · Filter by author tomgiarla opened on Jan 9, 2025
  3

• phyluce_assembly_assemblo_spades failing for some sequences

  faircloth-lab/phyluce#361 · Filter by author antnette opened on Jan 9, 2025
  1

• UCE names do not match error in uce-tutorial when using abyss assembler

  faircloth-lab/phyluce#359 · Filter by author mlosada323 opened on Dec 15, 2024
  2

• phyluce_assembly_assemblo_spades gives errors when running uce-tutorial

  faircloth-lab/phyluce#358 · Filter by author mlosada323 opened on Dec 12, 2024
  3

• "Cannot find the a fasta file" error

  faircloth-lab/phyluce#357 · Filter by author franztastic opened on Dec 11, 2024
  1

• How much sequencing data do I need?

  faircloth-lab/phyluce#356 · Filter by author BrigidaGallone opened on Nov 28, 2024
  2

• Grouping phased fasta files for phyluce_assembly_match_contigs_to_probes

  faircloth-lab/phyluce#355 · Filter by author rhyacotritonriot opened on Nov 26, 2024

• Using the by-locus function when exploding monolithic fasta

  faircloth-lab/phyluce#354 · Filter by author amateos1998 opened on Nov 6, 2024
  1

• Samples with multiple lane reads

  faircloth-lab/phyluce#351 · Filter by author jb23590 opened on Oct 28, 2024
  3

• AttributeError: 'NoneType' object has no attribute 'groups'

  faircloth-lab/phyluce#350 · Filter by author Genomics-Bhuwan opened on Sep 25, 2024
  4

• copy_and_build_index error in phyluce mapping

  faircloth-lab/phyluce#349 · Filter by author kmontana13 opened on Sep 16, 2024