EnglishFrenchSpanish

OnWorks favicon

rate4site - Online in the Cloud

Run rate4site in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command rate4site 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


rate4site - detector of conserved amino-acid sites

SYNOPSIS


rate4site [OPTIONS] -s <MSA FILE>

DESCRIPTION


The rate of evolution is not constant among amino acid sites: some positions evolve slowly
and are commonly referred to as "conserved", while others evolve rapidly and are referred
to as "variable". The rate variations correspond to different levels of purifying
selection acting on these sites. The purifying selection can be the result of geometrical
constraints on the folding of the protein into its 3D structure, constraints at amino acid
sites involved in enzymatic activity or in ligand binding or, alternatively, at amino acid
sites that take part in protein-protein interactions. Rate4Site calculates the relative
evolutionary rate at each site using a probabilistic-based evolutionary model. This allows
taking into account the stochastic process underlying sequence evolution within protein
families and the phylogenetic tree of the proteins in the family. The conservation score
at a site corresponds to the site's evolutionary rate.

METHODOLOGY


The sole obligatory input to Rate4Site is an MSA file. The program then computes a
phylogenetic tree that is consistent with the available MSA (the user can also input a
pre-calculated tree). It then calculates the relative conservation score for each site in
the MSA. This is carried out using either an empirical Bayesian method or a maximum
likelihood method (Pupko et al., 2002). The differences between the two methods are
explained in details in Mayrose et al (2004).

REFERENCES


Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. 2004. Comparison of site-specific rate-
inference methods: Bayesian methods are superior. Mol Biol Evol 21: 1781-1791.

OPTIONS


-s MSA_FILE
The input sequence file name. The following formats are supported: Mase, Molphy,
Phylip, Clustal, Fasta

-t The input tree file name (in Newick format)

-o OUTPUT_FILE
The results output file

-a Reference sequence name in the MSA. The conservation scores are printed based on the
amino-acids in this sequence.

-k The number of discrete Gamma categories

-m Evolutionary model. The following amino-acids models are supported:

DAY (-md), JTT (-mj), REV (-mr), aaJC (-ma), LG (-Ml), WAG (-Mw) .

For nucleotides, the following models are supported: JC (-mn), HKY (-Mh), Tamura92 (-Mt), GTR (-Mg).

-b Branch lengths optimization flag:

-bn = no Branch lengths optimization

-bh = optimization using a homogeneous model (no among-site-rate-variation)

-bg = optimization using a Gamma model

-i Rate inference method flag:

-Im = rates are inferred using the maximum likelihood method

-Ib = rates are inferred using the empirical Bayes method

-z Tree constructing method

zj = Neighbor-joining tree with Jukes-Cantor distances

zn = Neighbor-joining tree with maximum likelihood distances

-h Short help message

Use rate4site online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    PAC Manager
    PAC Manager
    PAC is a Perl/GTK replacement for
    SecureCRT/Putty/etc (linux
    ssh/telnet/... gui)... It provides a GUI
    to configure connections: users,
    passwords, EXPECT regula...
    Download PAC Manager
  • 2
    GeoServer
    GeoServer
    GeoServer is an open-source software
    server written in Java that allows users
    to share and edit geospatial data.
    Designed for interoperability, it
    publishes da...
    Download GeoServer
  • 3
    Firefly III
    Firefly III
    A free and open-source personal finance
    manager. Firefly III features a
    double-entry bookkeeping system. You can
    quickly enter and organize your
    transactions i...
    Download Firefly III
  • 4
    Apache OpenOffice Extensions
    Apache OpenOffice Extensions
    The official catalog of Apache
    OpenOffice extensions. You'll find
    extensions ranging from dictionaries to
    tools to import PDF files and to connect
    with ext...
    Download Apache OpenOffice Extensions
  • 5
    MantisBT
    MantisBT
    Mantis is an easily deployable, web
    based bugtracker to aid product bug
    tracking. It requires PHP, MySQL and a
    web server. Checkout our demo and hosted
    offerin...
    Download MantisBT
  • 6
    LAN Messenger
    LAN Messenger
    LAN Messenger is a p2p chat application
    for intranet communication and does not
    require a server. A variety of handy
    features are supported including
    notificat...
    Download LAN Messenger
  • More »

Linux commands

  • 1
    abidw
    abidw
    abidw - serialize the ABI of an ELF
    file abidw reads a shared library in ELF
    format and emits an XML representation
    of its ABI to standard output. The
    emitted ...
    Run abidw
  • 2
    abilint
    abilint
    abilint - validate an abigail ABI
    representation abilint parses the native
    XML representation of an ABI as emitted
    by abidw. Once it has parsed the XML
    represe...
    Run abilint
  • 3
    coresendmsg
    coresendmsg
    coresendmsg - send a CORE API message
    to the core-daemon daemon ...
    Run coresendmsg
  • 4
    core_server
    core_server
    core_server - The primary server for
    SpamBayes. DESCRIPTION: Currently serves
    the web interface only. Plugging in
    listeners for various protocols is TBD.
    This ...
    Run core_server
  • 5
    fwflash
    fwflash
    fwflash - program to flash image file
    to a connected NXT device ...
    Run fwflash
  • 6
    fwts-collect
    fwts-collect
    fwts-collect - collect logs for fwts
    bug reporting. ...
    Run fwts-collect
  • More »

Ad