DATA

The folder "data" contains the smaller data files for the morning session of day 2. However, we would advice you to use the data provided on SAGA as it will make the data transfer to your folder much faster.

SCRIPTS

The folder "scripts" contains all the scripts to be run on SAGA. However, we would advice you that you transfer them from SAGA as described in the exercise below.

LECTURE

The folder "Lecture" contains the lecture from this session.

• Paralogy

EXERCISE

1. For the TreSpEx analyses we first need to install some modules in your home directory as they are not included in the availables ones on SAGA.
   

   module load Perl/5.32.0-GCCcore-10.2.0
   export PERL_CPANM_HOME=/tmp/cpanm_$USER # this time the variable is a variable of the system and can be used as is.
   cpanm Statistics::LineFit
   cpanm --force Statistics::Test::WilcoxonRankSum
   export PERL5LIB=/cluster/home/$USER/perl5/lib/perl5:/cluster/home/$USER/perl5/:$PERL5LIB # this time the variable is a variable of the system and can be used as is.
   nano .bashrc
   copy the line from e) into the text editor at the end
   close the file and save it with the same name
   

2. For getting started, copy all data from the folder "Day2Morning" to your folder in the project area in SAGA.

   cd /cluster/projects/nn9458k/phylogenomics/$YOURNAME
   cp -r ../week1/Day2Morning .
   cd Day2Morning
   

3. First we need to get a tree with bootstrap values for each individual loci.
   

   cd SingleGenes
   sh SingleGene_Analyses.sh
   

4. For the actual paralogy screening, we need the program TreSpEx and the blast folder within it. We will also need a relaxed phylip file format for the alignment input.
   

   perl /cluster/projects/nn9458k/phylogenomics/week1/Programs/FASconCAT-G/FASconCAT-G_v1.05.pl -o -a -p -p -s
   cd ../
   cp -r /cluster/projects/nn9458k/phylogenomics/week1/Programs/TreSpEx/TreSpEx.v1.2_SAGA.pl /cluster/projects/nn9458k/phylogenomics/week1/Programs/TreSpEx/blast .
   

5. For the paralogy screening and cleaning you will run TreSpEx on the trees with bootstrap values.
   

   sbatch sbatch_TreSpEx_Paralogy.sh
   

6. The alignment files have been sorted into the folders "FilesPruned" and "FilesNotPruned" within the "Results" folder. They have to be concatenated into one file now.
   

   mkdir SingleGenesPara
   cp Results/FilesNotPruned/FcC_* Results/FilesPruned/FcC_* SingleGenesPara/
   cd SingleGenesPara
   cp ../../../week1/Programs/FASconCAT-G/FASconCAT-G_v1.05.pl .
   cp ../../Day1Afternoon/SingleGenes/sbatch_Concatenation.sh .
   

   • Modify the ".sh" file to fit your needs for this analysis

   sbatch sbatch_Concatenation.sh
   

7. Next you will run a tree reconstruction to assess effect this paralogy pruning approach.
   

   cd Supermatrix
   cp ../../sbatch_Supermatrix_Cleaned_tree.sh .
   

   • Check if the name of the supermatrix is fitting for your supermatrix. If not please change it accordingly.

   sbatch sbatch_Supermatrix_Cleaned_tree.sh
   

RESULTS

The folder "Results" contains the most important results from this session.