Package: LAST

LAST - Genome-Scale Sequence Comparison
Documentation
Web site	https://gitlab.com/mcfrith/last
	$doc/last/last-tuning.rst
	$doc/last/last-matrices.rst
	$doc/last/FAQ.rst
	$doc/last/last-repeats.rst
	$doc/last/last-seeds.rst
LAST Cookbook	$doc/last/last-cookbook.rst
Web site	http://last.cbrc.jp
Tutorial	$local/pkg/last/doc/last-tutorial.html
Installation instructions	$local/pkg/last/doc/last.html
Significance of alignments	$local/pkg/last/doc/last-evalues.html
Optimizing speed, sensitivity and disk space	$local/pkg/last/doc/last-tuning.html
Related publications	$local/pkg/last/doc/last-papers.html
Built-in scoring matrices	$local/pkg/last/doc/last-matrices.html
FAQ	$local/pkg/last/doc/FAQ.html
Repeat masking	$local/pkg/last/doc/last-repeats.html
Seeding schemes for initial matches	$local/pkg/last/doc/last-seeds.html
Data
Platforms:
Installation: BIRCH, local
Programs:
fasta-nr - Keep the first of identical sequences (after converting them to uppercase) 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 multiMito.sh - This script demonstrates using LAST and maf-join to construct multiple alignment of the human, mouse, chicken, and fugu mitochondrial genomes. parallel-fasta - parallel-fastq -