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 -