Genomes2Genes: A Progressive Cactus Gene Analysis Pipeline

Genomes2Genes converts Progressive Cactus graph alignments into validated coding-sequence alignments, supporting 22,376 candidate de novo genes among 45,491 lineage-specific genes in 21 Brassicaceae species plus 2 outgroups.

• Why it matters: Whole-genome alignments are widely used, but gene-level analyses of Progressive Cactus Hierarchical Alignment Format outputs are difficult, limiting reliable exon and coding-sequence comparisons across extant and reconstructed ancestors.
• What they did: The pipeline extracts exon alignment blocks, resolves atypical genomic jumps, stitches exons into transcripts, and audits start/stop codons and frameshifting indels with validation steps across any chosen genome region.
• The result: In the tested Brassicaceae alignment, 1,811 of the 22,376 candidates had complete evidence of enabler mutations, enabling identification and removal of problematic regions for species or gene phylogeny reconstruction.

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