What IndelExtractor can do
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Features
IndelExtractor can generate several alignment masks in addition to the Indel mask that is used to help the researcher identify and remove Indels and the ambiguous alignment surrounding them, prior to phylogenetic analysis. Because IndelExtractor is written in Perl, it is cross-platform compatible (except for some platform specific bugs) and is made avialable under the GNU General Public License.
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 handeling; you can using it simply for sequence and alignment file format conversions!
Compatible with major Operating Systems
While IndelExtractor should be compatible with most major Operating Systems (OS's) it has only been tested on Win98, WinXP, RedHat 8.0 (psyche) and RedHat Fredora (Core 1).
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 recognised by file extensions. Files must have a compatible file extension in order that IndelExtractor can accurately determine the correct file format. While Microsoft Windows platforms automatically add the correct extension by selecting a format in the "Save As" dialog box, other platforms (Linux/UNIX) may ask you to supply your own file extension when saving alignments.
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
IndelExtractors 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.
©2004-2005 Nathan Haigh