===== ATIAM 2014 Project - Molecular clock synthesis =====

==== Subject ====

You can find the complete document for the ATIAM 2014 Project - Molecular clock synthesis here\

=== Slides ===

Here are the slides to the project presentation
[[https://dl.dropboxusercontent.com/u/24122451/Cours_Projet.pdf| Slides]] ==== Source code ====

=== Multiple alignment softwares ===

In order to ease your pain, we downloaded and check the five best multiple alignment softwares currently used. For each of these, we include in the following a small description of the compilation procedure and also a list of useful parameters for the project. Note that a vast set of parameters is available for each software, which is why we also included the link to the complete documentation in this page. (We encourage you to perform full-scale evaluation of all parameters for all the softwares)

All these softwares use the FASTA input file format, for which an example can be seen here
http://prodata.swmed.edu/promals/info/fasta_format_file_example.htm

Most softwares rely on the BLAST matrix format for scoring matrix which can be seen here
ftp://ftp.ncbi.nih.gov/blast/matrices/
http://drive5.com/muscle/nucmx

Clustal Omega 1.2.1

  • Download the Clustal-Omega package (v1.2.1)
  • Install argtable2 (http://argtable.sourceforge.net/)
  • Configure and compile the code inside the package

./configure make make install

Complete help is available here: [[http://www.clustal.org/download/clustalw_help.txt Documentation]]

//Interesting parameters// -MATRIX=FILENAME Use a user-defined scoring matrix following BLAST format.

MAFFT 7.213

  • Download the MAFFT package (v7.213)
  • Configure and compile the code inside the package

cd core make clean all make install

Complete help is available here: [[http://mafft.cbrc.jp/alignment/software/tips0.html Tips]]

//Interesting parameters// --anysymbol accepts any type of symbol in input --matrix FILENAME Use a user-defined scoring matrix following BLAST format. All infos: mafft --man

MUSCLE 3.8.425

  • Download the MUSCLE package (v3.8.425)
  • Compile the code inside the package

make clean all

Complete help is available here: [[http://www.drive5.com/muscle/manual/ Manual]]

//Interesting parameters// -seqtype option accepts any type of symbol in input -matrix FILENAME Use a user-defined scoring matrix following BLAST format

ProbCons 1.12

  • Download the ProbCons package (v1.12)
  • Compile the code inside the package

make clean all

Complete help is available here: [[http://genome.cshlp.org/content/suppl/2005/02/01/15.2.330.DC1/manual.pdf Manual]]

//Interesting parameters// -m, --matrixfile FILENAME Read scoring matrix parameters from FILENAME //Warning this matrix is not in BLAST format, its format is detailed in the manual//

T-Coffee 6.18

  • Download the T-Coffee package (v6.18)
  • Compile the code inside the package

make clean all

Complete help is available here: [[http://www.tcoffee.org/Documentation/t_coffee/t_coffee_tutorial.htm Tutorial]]

//Interesting parameters// -matrix=FILENAME Use a user-defined scoring matrix following BLAST format.

=== MATLAB figures ===

Here are a few scripts offered to help you in producing high-quality figures.