SYNOPSIS
andi [-jlv] [-b INT] [-p FLOAT] [-m MODEL] [-t INT] FILES...DESCRIPTION
- andi estimates the evolutionary distance between closely related genomes. For this andi reads the input sequences from FASTA files and computes the pairwise anchor distance. The idea behind this is explained in a paper by Haubold et al. (see below).
OUTPUT
The output is a symmetrical distance matrix in PHYLIP format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). For technical reasons the comparison might fail and no estimate can be computed. In such cases nan is printed. This either means that the input sequences were too short (<200bp) or too diverse (K>0.5) for our method to work properly.OPTIONS
- -b, --bootstrap <INT>
- Compute multiple distance matrices, with n-1 bootstrapped from the first. See the paper Klötzl & Haubold (2016, in review) for a detailed explanation.
- -j, --join
- Use this mode if each of your FASTA files represents one assembly with numerous contigs. andi will then treat all of the contained sequences per file as a single genome. In this mode at least one filename must be provided via command line arguments. For the output the filename is used to identify each sequence.
- -l, --low-memory
- In multithreaded mode, andi requires memory linear to the amount of threads. The low memory mode changes this to a constant demand independent from the used number of threads. Unfortunately, this comes at a significant runtime cost.
- -m, --model <Raw|JC|Kimura>
- Different models of nucleotide evolution are supported. By default the Jukes-Cantor correction is used.
- -p <FLOAT>
- Significance of an anchor pair; default: 0.05.
- -t, --threads <INT>
-
The number of threads to be used; by default, all available processors are used.
Multithreading is only available if andi was compiled with OpenMP support. - -v, --verbose
- Prints additional information. Apply multiple times for extra verboseness.
- -h, --help
- Prints the synopsis and an explanation of available options.
- --version
- Outputs version information and acknowledgments.
COPYRIGHT
Copyright © 2014 - 2016 Fabian Klötzl License GPLv3+: GNU GPL version 3 or later.This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at <http://gnu.org/licenses/gpl.html>.
ACKNOWLEDGMENTS
1) andi: Haubold, B. Klötzl, F. and Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of evolutionary distances between closely related genomes2) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.
3) SA construction: Mori, Y. (2005). Short description of improved two-stage suffix sorting algorithm. http://homepage3.nifty.com/wpage/software/itssort.txt