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trimal
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public |
A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
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2024-08-28 |
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ucsc-bigwigsummary
|
public |
Extract summary information from a bigWig file.
|
2024-08-28 |
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meme
|
public |
Motif-based sequence analysis tools.
|
2024-08-28 |
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ucsc-catdir
|
public |
concatenate files in directory to stdout.
|
2024-08-27 |
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ucsc-hgloadoutjoined
|
public |
load new style (2014) RepeatMasker .out files into database
|
2024-08-27 |
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ucsc-bedremoveoverlap
|
public |
Remove overlapping records from a (sorted) bed file. Gets rid of
|
2024-08-27 |
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ucsc-maffetch
|
public |
get overlapping records from an MAF using an index table
|
2024-08-27 |
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ucsc-gff3togenepred
|
public |
convert a GFF3 file to a genePred file
|
2024-08-27 |
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ucsc-pslsort
|
public |
Merge and sort psCluster .psl output files
|
2024-08-27 |
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ucsc-bedrestricttopositions
|
public |
Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file.
|
2024-08-27 |
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ucsc-netsplit
|
public |
Split a genome net file into chromosome net files
|
2024-08-27 |
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ucsc-chainsort
|
public |
Sort chains. By default sorts by score.
|
2024-08-27 |
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ucsc-bigwigtobedgraph
|
public |
Convert from bigWig to bedGraph format.
|
2024-08-27 |
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ucsc-genepredtogtf
|
public |
Convert genePred table or file to gtf.
|
2024-08-27 |
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ucsc-pslcheck
|
public |
validate PSL files
|
2024-08-27 |
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ucsc-dbsnoop
|
public |
Produce an overview of a database.
|
2024-08-27 |
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ucsc-paranodestatus
|
public |
version 12.18
|
2024-08-27 |
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ucsc-hgloadout
|
public |
load RepeatMasker .out files into database
|
2024-08-27 |
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ucsc-hgloadwiggle
|
public |
Load a wiggle track definition into database
|
2024-08-27 |
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ucsc-maftoaxt
|
public |
Convert from maf to axt format
|
2024-08-27 |
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ucsc-psltobed
|
public |
transform a psl format file to a bed format file.
|
2024-08-27 |
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ucsc-mktime
|
public |
convert date string to unix timestamp
|
2024-08-27 |
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ucsc-parahubstop
|
public |
version 12.18
|
2024-08-27 |
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ucsc-expmatrixtobarchartbed
|
public |
Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
|
2024-08-27 |
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ucsc-mafsplitpos
|
public |
Pick positions to split multiple alignment input files
|
2024-08-27 |
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ucsc-mafaddirows
|
public |
add 'i' rows to a maf
|
2024-08-27 |
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ucsc-websync
|
public |
download from https server, using files.txt on their end to get the list of files
|
2024-08-27 |
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ucsc-pslsomerecords
|
public |
Extract multiple psl records
|
2024-08-27 |
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ucsc-para
|
public |
version 12.18
|
2024-08-27 |
|
ucsc-bedgeneparts
|
public |
Given a bed, spit out promoter, first exon, or all introns.
|
2024-08-27 |
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ucsc-autosql
|
public |
create SQL and C code for permanently storing
|
2024-08-27 |
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ucsc-psltopslx
|
public |
Convert from psl to pslx format, which includes sequences
|
2024-08-27 |
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ucsc-addcols
|
public |
Sum columns in a text file.
|
2024-08-27 |
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ucsc-genepredtoprot
|
public |
create protein sequences by translating gene annotations
|
2024-08-27 |
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ucsc-nettobed
|
public |
Convert target coverage of net to a bed file.
|
2024-08-27 |
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ucsc-chainnet
|
public |
Make alignment nets out of chains
|
2024-08-27 |
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ucsc-randomlines
|
public |
Pick out random lines from file
|
2024-08-27 |
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ucsc-catuncomment
|
public |
Concatenate input removing lines that start with '#'
|
2024-08-27 |
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ucsc-mafmefirst
|
public |
Move component to top if it is one of the named ones.
|
2024-08-27 |
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ucsc-farc
|
public |
Reverse complement a FA file
|
2024-08-27 |
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ucsc-chainprenet
|
public |
Remove chains that don't have a chance of being netted
|
2024-08-27 |
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ucsc-hggcpercent
|
public |
Calculate GC Percentage in 20kb windows
|
2024-08-27 |
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ucsc-pslrecalcmatch
|
public |
Recalculate match,mismatch,repMatch columns in psl file.
|
2024-08-27 |
|
ucsc-htmlcheck
|
public |
Do a little reading and verification of html file
|
2024-08-27 |
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ucsc-pslreps
|
public |
Analyze repeats and generate genome-wide best alignments from a
|
2024-08-27 |
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ucsc-chainfilter
|
public |
Filter chain files. Output goes to standard out.
|
2024-08-27 |
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ucsc-bedtobigbed
|
public |
Convert bed file to bigBed. (BigBed version: 4)
|
2024-08-27 |
|
ucsc-netsyntenic
|
public |
Add synteny info to net.
|
2024-08-27 |
|
ucsc-paranodestart
|
public |
version 12.18
|
2024-08-27 |
|
ucsc-twobitdup
|
public |
check to see if a twobit file has any identical sequences in it
|
2024-08-27 |
