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Ngila is a global alignment program that can align pairs of sequences using logarithmic and affine gap penalties.
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readme.txt

NGILA VERSION 1.3 - Logarithmic and Affine Sequence Alignments

Copyright (C) 2005-2010  Reed A. Cartwright - All rights reserved.

DESCRIPTION
  Ngila is a global alignment program that can align pairs of sequences using
  logarithmic and affine gap penalties.

REFERENCE
  Cartwright RA (2007) Ngila: global pairwise alignments with logarithmic and
  affine gap costs. Bioinformatics. 23(11):1427-1428

CONTACT
  reed@scit.us or racartwright@uh.edu

LICENSE
  GPL ver 3.  See copying.txt.

INSTALLATION
  Installation from source requires CMake (http://cmake.org/), Boost Libraries
  (http://boost.org/).  Binary packages are available.  To install on unix-like
  systems simply use
  
  cmake . && make && make install
  
  in the extracted source code directory.  On Windows you can use CMake GUI
  to create project files for Visual Studio and install from there.  More 
  detailed directions and help can be found on the website.

DOWNLOAD
  Ngila can be downloaded from the url <http://scit.us/projects/ngila/>, which
  is its development website.

COMMAND LINE USAGE
  ngila -m zeta -t 0.1 -k 2.0 -r 0.05 -z 1.65 sequences.fasta

  See 'ngila --help' for complete command line usage.

  See <http://scit.us/projects/ngila/> for more details on running ngila.

MODEL DESCRIPTIONS
  Ngila includes models of alignment based on evolutionary models. For a basic
  description of the evolutionary models see Cartwright RA (2009) "Problems and
  solutions for estimating indel rates and length distributions." Molecular
  Biology and Evolution, 26:473-480.  The models are as follows:
    zeta: DNA model with indel lengths following a power-law distribution
	geo:  DNA model with a geometric distribution
	aazeta: protein model (LG 2008) with a power-law distribution
	aageo: protein model with a geometric distribution
	cost: specify substitution and gap costs explicitly
	
INPUT FILES
  The input file has to be in FASTA, PHYLIP, or CLUSTAL format.  If more than two
  sequences are given then Ngila will align based on the 'pairs' option.

OUTPUT FILES
  Ngila has two types of output: sequence alignments and distance matrices.
  Supported sequence alignment formats are Clustal, Fasta, and Phylip.  Clustal
  is the default.  The format is read from the output file's extension or
  specified directly; "ngila -o seqs.fas" and "ngila -o fas:seqs.txt" both
  produce fasta output.  "ngila -o aln:-" sends Clustal formated sequence to
  stdout.  The following extensions are supported for distance matrices:
  dist-c = likelihood-based cost scores, dist-i = sequence identities, dist-d =
  sequence distances, dist = lower-triangle like dist-d and upper like dist-i.

SUBSTITUTION MATRIX
  Used by the "cost" model.  An example of the format can be seen in matrix/dna.

NGILARC
  Command-line options can be specified using an ngilarc file.  By default the
  program looks for $HOME/.ngilarc (unix) or %HOME%/ngilarc.txt (windows).  This
  file can contain long-form command line options like in the ngilarc.txt
  example file.
 

ALGORITHM
  Ngila implements a Miller and Myers (1988) candidate list method of sequence
  alignment with the gap cost being of the form g(x) = a + b*x + c*ln x.  Ngila
  will return the alignment with the minimum cost and has rules for breaking
  ties.  Ngila's main alignment algorithm is divide-and-conquer, which requires
  O(M) memory; but slower than a holistic, O(MN) memory algorithm.

  Ngila implements a secondary, holistic algorithm for alignment, which is
  faster.  The options -M and -N (-M is for the larger sequence) allow users to
  specify thresholds for when the holistic algorithm is used instead of the DnC
  algorithm.  For example, command 'ngila -M 5000 -N 5000 seqs.aln' will align
  the sequences in 'seq.aln' via the divide-and-conquer algorithm, but when
  subsequences less than or equal to 5000-5000 are being aligned, the holistic
  algorithm will be used.
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