// data dumped from keyset display

Category : "Comparative Genomics"
Package	 "LAST"
Program	 "last-bisulfite-paired.sh"
Program	 "last-bisulfite.sh"
Program	 "fastq-interleave"
Program	 "lastal"
Program	 "lastdb"
Program	 "last-dotplot"
Program	 "last-map-probs"
Program	 "last-merge-batches"
Program	 "last-pair-probs"
Program	 "last-postmask"
Program	 "last-split"
Program	 "last-train"
Program	 "maf-convert"
Program	 "maf-join"
Program	 "maf-sort"
Program	 "maf-swap"
Program	 "multiMito.sh"
Program	 "parallel-fastq"

File : "$doc\/last\/FAQ.html"
Description	 "FAQ"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/FAQ.html"

File : "$doc\/last\/last-evalues.html"
Description	 "Significance of alignments"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-evalues.html"

File : "$doc\/last\/last-matrices.html"
Description	 "Built-in scoring matrices"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-matrices.html"

File : "$doc\/last\/last-papers.html"
Description	 "Related publications"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-papers.html"

File : "$doc\/last\/last-repeats.html"
Description	 "Repeat masking"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-repeats.html"

File : "$doc\/last\/last-seeds.html"
Description	 "Seeding schemes for initial matches"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-seeds.html"

File : "$doc\/last\/last-tuning.html"
Description	 "Optimizing speed, sensitivity and disk space"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-tuning.html"

File : "$doc\/last\/last-tutorial.html"
Description	 "Tutorial"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last-tutorial.html"

File : "$doc\/last\/last.html"
Description	 "Installation instructions"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "$doc\/last\/last.html"

File : "http:\/\/last.cbrc.jp"
Description	 "Web site"
Pick_me_to_call	 "$ACE_FILE_LAUNCHER" "http:\/\/last.cbrc.jp"

Package : "LAST"
Description	 "Genome-Scale Sequence Comparison"
Category	 "Comparative Genomics"
Documentation	 "http:\/\/last.cbrc.jp"
Documentation	 "$doc\/last\/last-tutorial.html"
Documentation	 "$doc\/last\/last.html"
Documentation	 "$doc\/last\/last-evalues.html"
Documentation	 "$doc\/last\/last-tuning.html"
Documentation	 "$doc\/last\/last-papers.html"
Documentation	 "$doc\/last\/last-matrices.html"
Documentation	 "$doc\/last\/FAQ.html"
Documentation	 "$doc\/last\/last-repeats.html"
Documentation	 "$doc\/last\/last-seeds.html"
Program	 "last-bisulfite-paired.sh"
Program	 "last-bisulfite.sh"
Program	 "fastq-interleave"
Program	 "lastal"
Program	 "lastdb"
Program	 "last-dotplot"
Program	 "last-map-probs"
Program	 "last-merge-batches"
Program	 "last-pair-probs"
Program	 "last-postmask"
Program	 "last-split"
Program	 "last-train"
Program	 "maf-convert"
Program	 "maf-join"
Program	 "maf-sort"
Program	 "maf-swap"
Program	 "multiMito.sh"
Program	 "parallel-fasta"
Program	 "parallel-fastq"
BIRCH	

Program : "fastq-interleave"
Description	 "Read 2 fastq files, and write them interleaved"
Category	 "Comparative Genomics"
command	 "fastq-interleave x.fastq y.fastq"
Package	 "LAST"
Documentation	
BIRCH	

Program : "last-bisulfite-paired.sh"
Description	 "Aligning bisulfite-converted DNA reads to a genome"
Category	 "Comparative Genomics"
command	 "last-bisulfite.sh my_f my_r reads.fastq > results.maf"
Package	 "LAST"
Documentation	 "$doc\/last\/bisulfite.html"

Program : "last-bisulfite.sh"
Description	 "Aligning bisulfite-converted DNA reads to a genome"
Category	 "Comparative Genomics"
command	 "last-bisulfite.sh my_f my_r reads.fastq > results.maf"
Package	 "LAST"
Documentation	 "$doc\/last\/bisulfite.html"
BIRCH	

Program : "last-dotplot"
Description	 "Create a dotplot from a last alignment"
Category	 "Comparative Genomics"
command	 "last-dotplot [options] maf-or-tab-alignments dotplot.png"
Package	 "LAST"
Documentation	 "$doc\/last\/last-dotplot.html"
BIRCH	

Program : "last-map-probs"
Description	 "Calculate a mismap probability for each alignment."
Description	 "This is the probability\n\
that the alignment does not reflect the origin of the query sequence, assuming\n\
that one reported alignment does reflect the origin of each query."
Category	 "Comparative Genomics"
command	 "last-map-probs [options] lastal-alignments"
Package	 "LAST"
Documentation	 "$doc\/last\/last-map-probs.html"
BIRCH	

Program : "last-merge-batches"
Description	 "Read files of lastal output, merge corresponding batches, and write them"
Category	 "Comparative Genomics"
command	 "last-merge-batches files"
Package	 "LAST"
BIRCH	

Program : "last-pair-probs"
Description	 "Read alignments of paired DNA reads to a genome"
Description	 "and: (1) estimate the\n\
distribution of distances between paired reads, (2) estimate the probability\n\
that each alignment represents the genomic source of the read."
Category	 "Comparative Genomics"
command	 "last-pair-probs [options] interleaved-alignments"
command	 "last-pair-probs [options] alignments1 alignments2"
Package	 "LAST"
Documentation	 "$doc\/last\/last-pair-probs.html"
BIRCH	

Program : "last-postmask"
Description	 "Get alignments that have a segment with score >= threshold, with gentle\n\
masking of lowercase letters"
Category	 "Comparative Genomics"
command	 "last-postmask in.maf > out.maf"
Package	 "LAST"
Documentation	 "$doc\/last\/last-postmask.html"
BIRCH	

Program : "last-split"
Description	 "Read alignments of query sequences to a genome, and estimate the genomic\n\
source of each part of each query, allowing different parts of one query to\n\
come from different parts of the genome"
Category	 "Comparative Genomics"
command	 "last-split [options] LAST-alignments.maf"
Package	 "LAST"
Documentation	 "$doc\/last\/last-split.html"
BIRCH	

Program : "last-train"
Description	 "last-Try to find suitable score parameters for aligning the given sequences."
Category	 "Comparative Genomics"
command	 "last-train [options] lastdb-name sequence-file(s)"
Package	 "LAST"
Documentation	 "$doc\/last\/last-train.html"
BIRCH	

Program : "lastal"
Description	 "finds local alignments between query sequences, and reference sequences that have been prepared using lastdb"
Category	 "Comparative Genomics"
command	 "lastal [options] lastdb-name fasta-sequence-file(s)"
Package	 "LAST"
Documentation	 "$doc\/last\/lastal.html"

Program : "lastdb"
Description	 "Prepare sequences for subsequent alignment with lastal"
Category	 "Comparative Genomics"
command	 "lastdb [options] output-name fasta-sequence-file(s)"
Package	 "LAST"
Documentation	 "$doc\/last\/lastdb.html"
BIRCH	

Program : "maf-convert"
Description	 "Read MAF-format alignments & write them in another format"
Category	 "Comparative Genomics"
command	 "maf-convert axt mafFile(s)"
command	 "maf-convert blast mafFile(s)"
command	 "maf-convert blasttab mafFile(s)"
command	 "maf-convert html mafFile(s)"
command	 "maf-convert psl mafFile(s)"
command	 "maf-convert sam mafFile(s)"
command	 "maf-convert tab mafFile(s)"
Package	 "LAST"
Documentation	 "$doc\/last\/maf-convert.html"
BIRCH	

Program : "maf-join"
Category	 "Comparative Genomics"
command	 "maf-join sorted-file1.maf sorted-file2.maf ..."
Package	 "LAST"
BIRCH	

Program : "maf-sort"
Category	 "Comparative Genomics"
command	 "maf-sort [options] my-alignments.maf"
Package	 "LAST"
BIRCH	

Program : "maf-swap"
Description	 "Change the order of sequences in MAF-format alignments"
Category	 "Comparative Genomics"
command	 "maf-sort [options] my-alignments.maf"
Package	 "LAST"
BIRCH	

Program : "multiMito.sh"
Description	 "This script demonstrates using LAST and maf-join to construct multiple alignment of the human, mouse, chicken, and fugu mitochondrial genomes."
Category	 "Comparative Genomics"
command	 "multiMito.sh"
Package	 "LAST"
BIRCH	

Program : "parallel-fasta"
Package	 "LAST"
Documentation	 "$doc\/last\/last-parallel.html"
BIRCH	

Program : "parallel-fastq"
Category	 "Comparative Genomics"
Package	 "LAST"
Documentation	 "$doc\/last\/last-parallel.html"
BIRCH