Program Index

• ABySS - de novo sequence assembler
• acedemo - Demonstration laboratory database
• adaptercheck.py - Find potential read-through adapter contamination in sequencing reads
• align - Pairwise global sequence alignment
• Archaeopteryx - Archaeopteryx is the successor to ATV.
• artemis - DNA sequence annotation tool
• bachrest - Restriction site search (batch)
• beagle - Phasing genotypes and imputing ungenotyped markers
• birch - biolegato interface for launching BIRCH programs
• birchadmin - BIRCH administration tool
• birchdb - BIRCH documentation database
• birchenv.py - API methods for setting environment variables and platform detection
• birchhome.py - modify paths in BIRCH parameter files for local BIRCH system
• birchlib.py - Library functions for BIRCH utilities
• birchprops - Set and modify properties of the local BIRCH installation, found in $BIRCH/local/admin/BIRCH.properties
• birchscript.py - Library methods for BIRCH install-scripts
• BIRCHSettings.py - Change settings for BIRCH
• birchstats - Report statistics on BIRCH usage
• BIRCHUserSettings.py - Set User's environment variables for BIRCH
• bl_alias.py - For each file whose name begins with target, create a symbGiven a series of paired-end read filenames, replace the leftmost common string with a specified string
• bl_makelinks.py - Create symbolic links to files in another directory
• bl_rename.py - Given a series of filenames, replace the target string with newname string
• blast2gi.py - Given output from NCBI Blast+ using the -remote option , create a file containing GI numbers of hits listed in the output
• blast_formatter - convert blast output to a differrent format
• blastdbcmd - Client for local BLAST databases
• blastdbkit.py - Install and update local BLAST databases
• blastn - search DNA database using DNA query
• blastp - search protein database using protein query
• BlastViewer - view and analyze BLAST output
• blastx - search protein database using auto-translated DNA query
• blblastout.py - open BLAST output in a viewer or save the file
• bldna - biolegato interface for DNA/RNA sequence analysis
• BLExtractSubset.py - Extract a subset of sequences from a GDE flatfile
• blgeneric - run BioLegato with no menus and no canvas (for demonstration purposes)
• BLHelper.py - Set environment variables for BioLegato Helper Applications
• blmarker - bioLegato interface for discrete state data (eg. molecular markers)
• blnalign - biolegato interface for working with multiple DNA/RNA alignments
• blncbi - Graphical query program for NCBI databases
• blnfetch - BioLegato interface for retrieving DNA or RNA sequences from NCBI
• blpalign - biolegato interface for working with multiple protein alignments
• blpfetch - BioLegato interface for retrieving amino acid sequences from NCBI
• blprotein - biolegato interface for protein sequence analysis
• blreads - Process and analyze DNA sequencing reads
• blrevcomp - reverse-complement, reverse or complement a DNA or RNA strand
• blsort.py - Sort a BioLegato table
• bltable - Simple spreadsheet for generic data
• bltree - bioLegato interface for phylogenetic trees
• browser.csh - Launch a default browser from another application
• btail.py - Print the contents of a file beginning at line x
• cd-hit - reduce redundancy and cluster amino acid sequences
• cd-hit-2d - compare two protein sequence databases
• cd-hit-454 - Identify duplicates from 454 reads
• cd-hit-div - sort and divide sequence database into shorter files
• cd-hit-dup - remove duplicates from sequencing reads
• cd-hit-est - reduce redundancy and cluster nucleic acid sequences
• cd-hit-est-2d - compare two nucleotide sequence databases
• cd-hit-lap - Identify overlapping reads
• chooseviewer.py - choose a program for viewing a file
• clique - Compatability method for two-state characters
• clu2ig - Translate multiply aligned sequences in clustal format to Intelligenetics format
• clustalo - Multiple sequence alignment
• clustalw - Multiple sequence alignment
• clustalx - Multiple sequence alignment and editing
• Cn3D - Protein 3D structure viewer
• confadd - Add confidence information (eg. bootstrap) to a phylogenetic tree
• ConfirmBox2 - Opens a popup box with a question and Yes and No buttons.
• consense - Consensus trees
• contml - Gene Frequencies and Continuous Characters Maximum Likelihood
• contrast - compute contrasts for comparative method
• csv2phyl.sh - >>> csv2phyl.sh is obsolete. Instead, use phylcnv.py which handles a larger number of file formats
• cuffcompare - compare the transcriptomes assembled from different RNA-Seq libraries
• cuffdiff - Compare expression levels of genes and transcripts in RNA-Seq experiments
• cufflinks - assembles transcriptomes from RNA-Seq data and quantifies their expression
• cuffmerge - merge transcriptome assemblies into a master transcriptome
• cuffnorm - normalize the expression levels from a set of RNA-Seq libraries
• cuffquant - Quantify gene and transcript expression in RNA-Seq samples
• customdoc.py - String substitution for HTML files
• cutadapt - finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
• cytoscape - Cytoscape
• d3hom - Dot-matrix DNA similarity, k=3
• d4hom - Dot-matrix DNA similarity, k=4
• dapple - Image Analysis for DNA Microarrays
• dat2ace.py - Create ACeDB file objects for all data files in a directory
• decorator - decorate phylogentic trees with various data fields (such as sequence accessors, taxonomic scientific names) and write them in phyloXML format
• delgi.py - remove GI numbers from GenBank flatfiles, in compliance with the NCBI phase out of GI numbers
• dGDE - GDE interface for leash
• dialign-tx - segment-based multiple alignment
• dipspades - assembler for highly polymorphic diploid genomes
• DirChooser2 - Opens a file chooser, and prints the fully-qualified path of the selected directory.
• dnacomp - DNA phylogeny using compatability method
• dnadist - Construct distance matrix for DNA sequences
• dnainvar - DNA sequence phylogeny invariants
• dnaml - DNA phylogeny using Maximum Likelihood
• dnamlk - DNA phylogeny using Maximum Likelihood (with evolutionary clock)
• dnamove - DNA parsimony with interactive tree rearrangement
• dnapars - DNA parsimony
• dnapenny - DNA parsimony using branch and bound method
• doc2ace.py - Create ACeDB file objects for all documenataion files in a directory
• dollop - Discrete data parsimony method of DOLLO
• dolmove - Interactive Dollo and Polymorphism Parsimony
• dolpenny - Branch and bound parsimony using Dollo and polymorphism methods
• dotter - Dotmatrix comparison for DNA and Protein sequences
• drawgram - Draw cladograms
• drawtree - Draw radial trees
• ErrorBox2 - Opens a popup error box with a message and an Okay button.
• ExpressConverter - Convert microarray files to TIGR file formats
• factor - Generate discrete (0,1) characters from multistate characters
• fasta - Sequence database similarity
• fasta-nr - Keep the first of identical sequences (after converting them to uppercase)
• fastalen.py - separate fasta sequences by length
• fastf - compare mixed peptides to a protein database
• fastm - compare ordered peptides (or short DNA sequences) to a protein or DNA database
• fastq-interleave - Read 2 fastq files, and write them interleaved
• fastq_pair - Remove non-paired reads from left or right read files
• FastQC - A quality control tool for high throughput sequence data.
• fasts - compare unordered peptides to a protein database
• fastx - Database similarity - allow frameshifts between codons
• fasty - Database similarity - Allow frameshifts within codons
• features - extract features from GenBank flatfile entries
• fetch - retrieve entries from local flatfile database by name or accession number
• fil.py - create .fil files for use by FASTA
• findkey - Keyword search on local flatfile database
• fitch - Distance trees - Fitch/ Margoliash
• fixfq.py - Divide a fastq file into two files, one with validated reads, and the other with reads that do not comply with the fastq format
• flat2phyl - Convert a GDE flatfile into a Phylip discrete character file
• fromgb -
• funnel - Reformats a free-format or FASTA-format file to a fixed line-length, preserving comments that begin with a semicolon (;)
• garnier - Protein secondary structure
• Gblocks - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
• Gblocks.py - Wrapper to run Gblocks from BioLegato
• gde - Genetic Data Environment
• gel - Given migration distances for standards of know size, calculate sizes of unknown fragments
• gendist - Compute genetic distances from gene frequencies
• genographer - Score markers from gel images
• getloc - retrieve entries from a local flatfile database
• getob - Parse features from GenBank flatfiles
• gffcompare - compare, merge, annotate and estimate accuracy of one or more GFF files
• gffread - Filters and/or converts GFF3/GTF2 records
• ggsearch - global alignment of two DNA or protein sequences
• glsearch - global alignment of DNA or protein query sequence with local alignments of database sequences
• grease - Protein hydrophobicity
• gstat.py - Calculates amino acid frequencies and other statistics for one or more proteins
• gtf_2_sam - convert gtf files to sam files
• guesspairs.py - Given a list of sequencing read files, make a guess as to which pairs of files should be grouped together as left and right read files
• hisat2 - Align RNAseq reads to a hisat2-indexed genome
• hisat2-build - Build an index of a genome for use by hisat2
• hisat2-inspect - print FASTA records from a hisat2 index in fields specified by options
• htmldoc.py - Create BIRCH HTML documentation from BIRCH and local databases
• intrest - Restriction site search
• Jalview - Multiple alignment viewer
• jellyfish - A fast k-mer counter
• kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
• l-gbirchdb - >>>>It is used for editing the copy of lbirchdb in local-generic. When a NEW BIRCH install is done, this empty database becomes the lbirchdb database.
• lalign - Rigorous local pairwise alignment
• 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
• lbirchdb - Database for local documentation
• lgbirchdb - Empty database to be used for local-installed documentation
• lucy - Assembly Sequence Cleanup Program
• 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
• mafft - Multiple sequence alignment by fast Fourier Transformation
• magic - MicroArray Genome Imaging and Clustering Tool
• magicblast - search for reads which match a custom sequence database
• makeblastdb - Create a BLAST-compatible database file from other formats
• MakeCons - Create a consensus sequence from a multiple alignment
• makelinks.sh - Create symbolic links in the current directory, pointing to files in a source directory
• makemenus.py - (deprecated) Create .GDEmenus files for all platforms
• map_db - read a FASTA (0), GENBANK flat file (1) PIR/VMS (5) or GCG binary (6) sequence database and produce the offsets necessary for efficient memory mapping
• Mapmaker - Create genetic maps using marker and phenotype data
• MapmakerQTL - Create maps for QTL data
• Mauve - Multiple Genome Alignment
• maxalign - Maximizing the size of gap-free columns by selecting an optimal subset of sequences in an alignment
• mesquite - A modular system for evolutionary analysis
• mGDE - GDE interface for discrete state data (eg. molecular markers)
• midas - Microarray Data Analysis System
• mix - Mixed method discrete character parsimony
• move - Interactive mixed-method parsimony
• mrbayes - Bayesian inference of phylogeny
• mrtrans - Align DNA sequences to a protein multiple alignment
• multidigest - Calculates restriction sites, fragments and fragment ends for multiple enzyme digests, complete or partial
• multiMito.sh - This script demonstrates using LAST and maf-join to construct multiple alignment of the human, mouse, chicken, and fugu mitochondrial genomes.
• MWCalculator - Calculate molecular weights for oligonucleotides
• ncbiquery.py - Send an Entrez query to NCBI and return the result
• neighbor - Distance trees - Neighbor-Joining/UPGMA
• numseq - Sequence dislpay and manipulation
• OkayBox2 - Opens a popup box with a message and an Okay button.
• osp - Oligonucleotide Search Program
• ospX - Oligonucleotide search program
• p1hom - Dot-matrix protein similarity, k=1
• p2hom - Dot-matrix protein similarity, k=2
• pal2nal.pl - align DNA to a protein alignment
• parallel-fasta -
• parallel-fastq -
• pars - Discrete character parsimony
• penny - Branch and bound parsimony for discrete data
• phyl2flat - Convert a Phylip discrete character file into a GDE flatfile
• phylcnv.py - Convert Phylip files to and from other formats
• phylip.py - Classes used by Python scripts that run Phylip programs
• phylo_win - Phylogenetic analysis workbench
• phyloXMLconverter - convert various phylogentic tree formats to phyloXML
• pigz - A parallel implementation of gzip for modern multi-processor, multi-core machines
• pima - Pattern-induced multiple sequence alignment
• pollux - DNA sequence read correction for all sequencing platforms
• primer3_core - Design oligonucleotide primers and probes
• proml - protein phylogeny using maximum likelihood
• promlk - protein phylogeny by maximum likelihood, constant evolutionary clock
• prot2nuc - Reverse translate protein to degenerate DNA
• protdist - Construct distance matrix for protein sequences
• protpars - Protein parsimony
• pyc.py - compile a Python script into bytecode and creates pydoc HTML documentation
• quast - Evaluate genome assemblies
• randseq - Randomize a set of sequences
• Rcorrector - Adjusts threshold for trusted kmers based on kmer frequency
• readseq - Convert sequence files to other formats
• reform - print a multiple alignment using plain text
• relate - Statistical significance of database similarity
• restdist - Compute distance matrices for discrete data
• restml - Maximum likelihood phylogeny for discrete data
• retree - Rearrange and reroot phylogenetic trees
• ribosome - Translate nucleic acid to protein
• rmlauncher.py - removes platform-specific BIRCH launcher from user's desktop
• rnaspades - SPAdes Transcriptome Assembly
• ruler - Print a text ruler for use in numbering columns
• salmon - transcript quantification for RNA-seq data
• samtools - Utilities for the Sequence Alignment/Map (SAM) format
• seqboot - Create resampled datasets
• seqfetch.py - Given a set of GI (UID) or ACCESSION numbers , create a file containing the corresponding sequence entries
• seqkit - FASTA/Q file manipulation
• sequin - Annotate and submit sequences to GenBank
• SOAPdenovo-Trans - Transcriptome assembly
• SOAPdenovo2 - denovo genome assembler
• spades - Genome assembler
• splitdb - split a GenBank flatfile into a database containing annotation, sequence and index
• ssearch - Rigorous Smith-Waterman database similarity search
• stem - Short Time-series Expression Miner
• stringtie - assemble RNA-seq alignments into transcripts
• tace - text interface to ACeDB
• taxfetch.py - Given a set of ACCESSION numbers create a file containing the corresponding NCBI taxonomy entries
• tbl2asn - automates the creation of sequence records for submission to GenBank
• tblastn - search auto-translated DNA database using protein query
• tblastx - search auto-translated DNA database using auto-translated DNA query
• testcode - Find protein coding regions using method of Fickett
• tfastf - compare mixed peptides to a translated DNA database
• tfasts - compare unordered peptides to a translated DNA database
• tfastx - compare a protein to a DNA database, calculating similarities with frameshifts
• tfasty - compare a protein to a DNA database, calculating similarities with frameshifts
• tGDE - GDE interface for phylogenetic trees
• TIGR_Assembler - Assemble contigs
• tmev - TIGR Multi-Experiment Viewer
• TraceView - Sequence chromatogram viewer
• transrate - de-novo transcriptome assembly quality analysis
• treedist - Calculate distance between trees
• trim_galore - sequenc quality trimming and adaptor removal
• Trimmomatic - Trim adaptors from sequencing reads
• Trinity - RNA-Seq De novo Assembly
• truspades - assembler for short reads produced by Illumina TruSeq Long Read technology
• ugene - Ugene interface
• UNINSTALL-birch.py - Uninstall a BIRCH system
• uniqid.py - Encodes long names of sequences in a fasta file into short, unique numerical strings. Decodes file generated from encoded files, and restores original sequence names
• v_concat - Concatenates a set of sequence alignments.
• v_demograph - Estimates demographic parameters (effective population size, growth rate) by maximizing the coalescent prior for a single given clocklike tree.
• v_disttree - Tree methods dealing with distance matrices.
• v_evolve - Generates artificial data sets for a tree and a model of sequence evolution (available models are the same as in MLTREE and MLDIST)
• v_mldist - Computes pairwise maximum-likelihood distance matrices for nucleotide, amino acid, and two-state data under a variety of substitution models
• v_mltree - Computes likelihoods of trees under a variety of substitution models (see MLDIST)
• v_reroot - Reads a treefile (NH format) and reroots the tree, making node the new root.
• v_rewrite - Reads a data set and reformats it into various formats
• v_showtree - Reads treefile (NH format), generates ASCII picture, and computes distance matrix induced by branch length.
• v_splitcodon - Separate 1st, 2nd, 3rd codon positions of an alignment into separate file.
• v_treecomp - Reads two trees, each from a different file, and computes the Robinson Foulds score (topological distance measure based on splits).
• WebLogo - create sequence logos
• weighbor - weighted neighbor joining
• xace - Graphic interface to ACeDB
• xland - Sequence Landscapes
• xtract - converts XML into a table of data values
• xylem_identify - used by FINDKEY to extract LOCUS names from database hits
• xylem_shuffle - randomize sequences using a sliding window