category: Comparative Genomics

programs:

• beagle - Phasing genotypes and imputing ungenotyped markers
• fastq-interleave - Read 2 fastq files, and write them interleaved
• last-bisulfite-paired.sh - Aligning bisulfite-converted DNA reads to a genome
• last-bisulfite.sh - Aligning bisulfite-converted DNA reads to a genome
• last-dotplot - Create a dotplot from a last alignment
• last-map-probs - Calculate a mismap probability for each alignment.
• last-merge-batches - Read files of lastal output, merge corresponding batches, and write them
• last-pair-probs - Read alignments of paired DNA reads to a genome
• last-postmask -
• last-split -
• last-train - last-Try to find suitable score parameters for aligning the given sequences.
• lastal - finds local alignments between query sequences, and reference sequences that have been prepared using lastdb
• lastdb - Prepare sequences for subsequent alignment with lastal
• maf-convert - Read MAF-format alignments & write them in another format
• maf-join -
• maf-sort -
• maf-swap - Change the order of sequences in MAF-format alignments
• magicblast - search for reads which match a custom sequence database
• multiMito.sh - This script demonstrates using LAST and maf-join to construct multiple alignment of the human, mouse, chicken, and fugu mitochondrial genomes.
• parallel-fastq -