:: DESCRIPTION
Use Prob2plinkbig to convert large MACH probability files to PLINK dosage files.
::DEVELOPER
CTG (Complex Traits Genetics) Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
FastaFormat: Convert tab-delimited files into fasta format. Includes a quality score safe option (-q) for converting quality score files.
FastQFormat: Convert tab-delimited sequence and quality score files into fastQ format.
UnFastaFormat: Convert fasta files into tab-delimited format. Includes a quality score safe option (-q) for converting quality score files.
UnFastQFormat: Convert fastq files into tab-delimited format. Outputs sequences and quality scores into separate files. Edits sequence titles. Support for NCBI and Illumina formats.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TableParser: Simple tool for extracting sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parses out contigs, singletons, and assembled reads into separate files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Snowhite is a pipeline designed to flexibly and aggressively clean sequence reads (gDNA or cDNA) prior to assembly. It takes in and returns fasta formatted sequence and (optionally) quality files.
::DEVELOPER
The Dlugosch Lab @ The University of Arizona
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
Barker MS, Dlugosch KM, Dinh L, Challa RS, Kane NC, King MG, Rieseberg LH.
Evol Bioinform Online. 2010 Oct 20;6:143-9. doi: 10.4137/EBO.S5861.
:: DESCRIPTION
MoSeC (Model to Sequence Converter) is a Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence.
::DEVELOPER
Interdisciplinary Computing and Complex BioSystems (ICOS) research group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Apr 1;27(7):973-9. doi: 10.1093/bioinformatics/btr048. Epub 2011 Feb 4.
Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A.
:: DESCRIPTION
nxtrim: Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
NxTrim: optimized trimming of Illumina mate pair reads.
O’Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ.
Bioinformatics. 2015 Feb 5. pii: btv057
:: DESCRIPTION
mega_nexus is a program for converting MEGA input files to Splitstree input files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TABLE takes the output from MLINK or LINKMAP and tabulates it in a more easily digestible form. It can also produce files suitable for graphing lod scores and for input to HOMOG, BTEST and FASTMAP.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
blast2malign is an easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
