fastga for Mac

FastGA: A Fast Genome Aligner

_Authors: Gene Myers & Chenxi Zhou_ _First: May 10, 2023_ _Last: December 30, 2025_ FastGA Compare two genomes or a genome against itself and output a .1aln, .paf, or .psl file of all alignments found. Sub-Process Routines FAtoGDB: Convert a FASTA or ONEcode sequence file into a genome database (GDB) GIXmake: Build a genome index (GIX) for a given GDB ALNtoPAF: Stream PAF formatted alignments for a given .1aln file ALNtoPSL: Stream PSL formatted alignments for a given .1aln file Viewing Utilities GDBshow: Display select contigs or substrings thereof from a GDB GDBstat: Display various statistics and histograms of the scaffolds & contigs in a GDB ANOshow: Display annotation intervals of select contigs or subranges thereof from an ANO file ANOstat: Display various statistics and histograms of about the intervals in an ANO file GIXshow: Display range of a GIX ALNshow: Display selected alignments in a .1aln file in a variety of forms ALNplot: Display alignments in a .1aln or .paf file in a static collinear plot Additional Utilities GDBtoFA: Converts a GDB back to the FASTA or ONEcode sequence file it was derived from BEDtoANO: Convert a BED formatted file to a .1ano-file ANOtoBED: Convert an ANO file to a BED file PAFtoALN: Convert a PAF formatted file with X-CIGAR strings to a .1aln file PAFtoPSL: Convert a PAF formatted file with X-CIGAR strings to a .psl file GIXrm: Remove GDBs and GIXs including their hidden parts GIXcp: Copy GDBs and GIXs including their hidden parts as an ensemble GIXmv: Move GDBs and GIXs including their hidden parts as an ensemble ALNchain: Alignment filtering by construction of local chains ALNreset: Reset a .1aln file's internal references to the GDB(s) it was computed from C-Library for Accessing .1aln Files Error Handling .1aln File Reader Genome Database (GDB) Alignment Records Error Messages

Version 1.5 (December 30, 2025) ONEcode ANO Files

The addition of soft masking in V1.3 has lead to the development of a ONEcode version of a BED file, called an ANO- or .1ano-file, that records a collection of (oriented) intervals on a genome, along with a possible label and/or score for each annotation. There are new routines ANOshow, ANOstat, ANOtoBED, and BEDtoANO for showing the contents of a .1ano file, giving summary statistics about an .1ano file, and converting between BED files and .1ano files, respectively.