What IndelExtractor can do

Feature List

• Can run in GUI and command-line modes
• Identify Indels and ambiguous alignment surrounding them (Indel Mask)
• Jagged alignment ends added to Indel Mask (but not included as indels)
• Identification of invariable sites (Invariable Sites Mask)
• Identification of variable sites (Variable Sites Mask)
• Generation of a consensus sequence (Consensus Mask)
• Support for BLASTing sequences at NCBI (BLAST options available via the preferences)
• Support for aligning sequences utilising clustalw installed locally (clustalw options available via the preferences)
• Customisable GUI fonts
• Identification of partial sequences
• Basic alignment editing
• Residue Colouring
• View/hide panes on the main page
• Adjuster bars between id's and sequences
• Help bubbles
• Customise default mask options and output file formats
• Extensive sequence file format support:
  • ace Ace database
  • bsml - Bioinformatic Sequence Markup Language
  • embl - EMBL database
  • fasta - FASTA
  • fastq - Sanger Centre format with quality data
  • gcg - GCG
  • genbank - GenBank
  • phd - Phred
  • pir - PIR database
  • raw - plain text
  • scf - Standard Chromatogram Format
  • swiss - SwissProt

• Extensive alignment file format support:
  • clustalw - clustalw format
  • emboss - EMBOSS water and needle format^‡
  • fasta - FASTA format
  • maf - Multiple Alignment Format^‡
  • mega - MEGA format
  • meme - MEME format^‡
  • msf - msf (GCG) format
  • nexus - Swofford et al. NEXUS format
  • pfam - Pfam sequence alignment format
  • phylip - Felsenstein's PHYLIP format
  • psi - PSI-BLAST format
  • selex - selex (hmmer) format
  • ^‡Output format not supported

• Completely free for any use. See license.
• More

©2004-2005 Nathan Haigh