IndelExtractor 2.2.2

IndelExtractor is an application that generates different alignment masks in addition to an Indel's mask.
A molecular sequence alignment is the foundation of molecular phylogenetic analysis, yet is often one of the least considered aspects. Alignments often contain positions that are difficult to align (i.e. Indel regions) which may be "edited by eye" or removed prior to the analysis.

IndelExtractor is a GUI and command-line application written in Perl that generates various alignment masks in addition to an Indel's mask for easy identification and removal of Indels and their surrounding ambiguous alignment. The alignment masks are used to save 'masked' and/or 'unmasked' positions of an alignment to many different file formats.

IndelExtractor utilises the power of Bioperl for handling many sequence and alignment input/output file formats and for general sequence handling and manipulation. As a result of IndelExtractor's powerful file format handling; you can use it simply for sequence and alignment file format conversions!

Here are some key features of "IndelExtractor":


Input/Output Formats

IndelExtractor utilises the power of Bioperl for handling many sequence and alignment input/output file formats and for general sequence handling and manipulation. Therefore, many sequence and alignment file formats are supported, and they are recognized by file extensions. Files must have a compatible file extension in order that IndelExtractor can accurately determine the correct file format.

Alignment Masks

IndelExtractor was initially developed to help automate the task of Indel identification and removal. For this, the Indel mask was developed, whereby each position in the alignment was represenced by a character in a consensus style sequence to identify positions that formed part of an indel (masked regions) and those that did not (unmasked regions). However, additional masks are now available: invariable, variable and consensus masks. Once a mask has been generated, it can be used to save sub-alignments (masked/unmasked positions) to file, or as additional information in the more information rich alignment formats (e.g. NEXUS) when saving the whole alignment to file.

Auxiliary Features

IndelExtractor's feature set has been extended to allow alignment of sequences using clustalw to be undertaken from within IndelExtractor and the ability to BLAST sequences against the NCBI databases; options for both being available via IndelExtractor's preferences.

last updated on:
October 23rd, 2007, 17:08 GMT
price:
FREE!
homepage:
indelextractor.sourceforge.net
license type:
GPL (GNU General Public License) 
developed by:
IndelExtractor Team
category:
ROOT \ Science and Engineering \ Bioinformatics
IndelExtractor
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