EnglishFrenchSpanish

Ad


OnWorks favicon

andi - Online in the Cloud

Run andi in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command andi that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


andi - estimates evolutionary distance

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 <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, 2015 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 genomes
2) 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

Use andi online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Image Downloader
    Image Downloader
    Crawl and download images using
    Selenium Using python3 and PyQt5.
    Supported Search Engine: Google, Bing,
    Baidu. Keywords input from the keyboard
    or input from ...
    Download Image Downloader
  • 2
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    discussio...
    Download Eclipse Tomcat Plugin
  • 3
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 4
    GenX
    GenX
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 5
    pspp4windows
    pspp4windows
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 6
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • More »

Linux commands

Ad