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https://github.com/zkamvar/fitmodel

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https://github.com/zkamvar/fitmodel

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README 

        



== INSTALATION ==



On UNIX-like operating system (i.e., Mac OS X  and Linux), type the following commands in a terminal

window:



./configure;

make clean;

make;



In order  to install the program  'coltree' that will help  you visualise the results  of a fitmodel

analysis, type the following commands:



./configure  --enable-coltree;

make clean;

make;



== DESCRIPTION ==



'Fitmodel' estimates the  parameters of various codon-based models  of substitution, including those

described in  Guindon, Rodrigo, Dyer and Huelsenbeck  (2004). These models are  especially useful as

they accommodate site-specific switches between selection  regimes without a priori knowledge of the

positions in the tree where changes of selection regimes occurred.



The program  will ask for  two input files:  a tree file  and a sequence  file.  The tree  should be

unrooted  and in  NEWICK format.   fitmodel will  crash  if you  feed him  with a  rooted tree.  The

sequences  should be  in  PHYLIP interleaved  or  sequential format.   If you  are  planning to  use

codon-based models, the sequence length should be a  multiple of 3.  The program provides four types

of codon models:  M1, M2, M2a, and M3 (see  PAML manual).  Moreover, M2, M2a and  M3 can be combined

with  'switching' models  (option  'M').  Two  switching  models  are implemented:  S1  and S2.   S1

constraints the  rates of changes  between dN/dS values  to be uniform  (e.g., the rates  of changes

between negative and positive selection is constrained to  be the same as the rate of change between

neutrality  and positive  selection) while  S2 allows  for differents  rates of  change between  the

different classes of dN/dS values.



If  you are  using  a 'switching'  model,  'fitmodel' will  output file  with  the follwoing  names:

your_sequence_file_trees_w1,     your_sequence_file_trees_w2,     your_sequence_file_trees_w3    and

your_sequence_file_trees_wbest.  The w1, w2 and w3  files give the estimated tree with probabilities

of w1, w2,  and w3 (three maximum likelihood  dN/dS ratio estimates) calculated on each  edge of the

tree and  for each  site.  Hence, the  first tree in  one of  these files reports  the probabilities

calculated at the first  site of the alignment. Instead of probabilities,  the wbest file allows you

to identify  which of the tree  dN/dS is the most  probable on any give  edge, at any  given site. A

branch with label  0.0 means that w1  is the most probable class,  0.5 indicates the w2  is the most

probable and 1.0 means that w3 has the highest posterior probability.



Processing  those results  manually can  be very  tedious.  The  program 'coltree'  reads 'fitmodel'

output file  and generates a postscript  file which displays the  phylogeny at each  codon site with

different colors on edges depending on the posterior probabilities estimated on each branch, at each

site (see file p1.pdf).   This is very useful to detect site  specific changes of selection regimes.

To compile 'coltree' on UNIX-like systems, simply type the following commands in a terminal window:



This will generate the binary for 'coltree'. 'coltree' is a command-line program that takes as first

argument 'fitmodel' output tree  file. The second argument is the name  of the postscript file where

the trees will be written.



== EXAMPLE ==



The directory  example/ contains  a sequence file  (p1.nxs) and  a tree file  (p1.tree) that  can be

processed  by  fitmodel.  The  files  p1.nxs_fitmodel_stats, p1.nxs_fitmodel_tree,  p1.nxs_trees_w1,

p1.nxs_trees_w2,  p1.nxs_trees_w3 and  p1.nxs_trees_wbest  were generated  by  'fitmodel' using  the

M2a+S1 model.  The command line that was used in order to generate those files is the following one:



./fitmodel < param



where 'param'  is a text  file that contains  the series of  letters one have  to enter in  order to

select the M2a+S1 model (and other options) through the PHYLIP-like interface.



The file 'tree.ps' is  a postscript file that displays the posterior probability  of w1 on each edge

at each code site of the alignment. It was generated using the following command-line:



./coltree p1.nxs_trees_w1 tree.ps



====



Need more help? Contact me: [email protected]



BIBLIOGRAPHY



"Modeling the site-specific variation of selection patterns along lineages"

Stephane Guindon, Allen G Rodrigo, Kelly A Dyer, John P Huelsenbeck

Proceedings of the National Academy of Sciences of the United States of America

2004



"Modelling the variability of evolutionary processes"

Olivier Gascuel, Stephane Guindon

Reconstructing evolution. New mathematical and computational advances.

Oxford University Press

2007