`conda activate phylo`
Go to home directory if you are not there
This command is to clone the phyloscripts from github repository

git clone https://github.com/mossmatters/phyloscripts.git
python ~/phyloscripts/phypartspiecharts/reroot_trees.py

### Reroot tree
My outgroup here is core fila

python ~/phyloscripts/phypartspiecharts/reroot_trees.py astral_spp.tre outgroup.txt > astral_rooted.tre
python ~/phyloscripts/phypartspiecharts/reroot_trees.py gene_33.tre outgroup.txt > gene_33rooted.tre
python ~/phyloscripts/phypartspiecharts/reroot_trees.py gene_50.tre outgroup.txt > gene_50rooted.tre

### Installing phyparts
I already have git installed though

conda install mvn3 java git
conda install maven openjdk
git clone https://bitbucket.org/blackrim/phyparts.git

Go to your home directory where the phyparts is then run the commands below

./mvn_cmdline.sh
java -jar target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar

cd to lustre where all the rooted species and gene tree is

java -jar ~/phyparts/target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar phyparts -a 1 -d gene_50rooted.tre  -m astral_rooted.tre -o Xanthisma_phyparts

java -jar ~/phyparts/target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar phyparts -a 1 -d gene_33rooted.tre  -m astral_33rooted.tre -o Xanthisma_phyparts

java -jar ~/phyparts/target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar phyparts -s astral_rooted.tre -m gene_50rooted.tre -o Xanthisma_phyparts

### Discovista

conda create -n discovista_env python=3.8 -y
conda activate discovista_env
conda install -c conda-forge ete3 matplotlib pandas numpy biopython -y

I got an error with ```pip install discovista```
Hence I ```mkdir Discovista``` in Hybpiperoutput thn the following

cd DiscoVista
pip install dendropy --user
python /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils/discoVista.py \
  -s /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Phyparts/astral_rooted.tre\
  -g /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Phyparts/gene_50rooted \
  -o /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista

cd /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils

python /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils/discoVista.py \
-s /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Phyparts/astral_rooted.tre \
-g /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Phyparts/gene_50rooted \
-o /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista

python /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils/discoVista.py \
  -p /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/astral_rooted.tre \
  -g /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/gene_50rooted 
  -o /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/
  python /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils/discoVista.py \
  -t /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/astral_rooted.tre \
  -g /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/gene_50rooted \
  -o /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/
  
  python /path/to/discoVista.py \
  -t /path/to/species_tree.tre \
  -g /path/to/gene_trees_directory/ \
  -o /path/to/output_directory/

python /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils/discoVista.py \
-m 0 \
-c /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/splits.txt \
-p /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/astral_rooted.tr \  -o /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/

python /path/to/discoVista.py \
-m 0 \
-p /path/to/species_tree.tre \
-c /path/to/splits.txt \
-o /path/to/output_directory/

python /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/src/utils/discoVista.py \
-m 0 \
-c /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/splits.txt \
-p /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/astral_rooted \
--threshold 97 \
-o /lustre/scratch/oshodipo/Xanthisma/Hybpiperoutput/Discovista/DiscoVista/
python /home/joh97948/scripts/replace_taxon_names.py astral_33rooted.tre Change_nodesrecent.csv > astral_rooted_33renamed.tre