Project to find origins of parasitism in a pylogenetic tree of live.

connect to the VM (via Cygwin64):

ssh name@h -L 127.0.0.1:8529:127.0.0.1:8529 -p 15351 -q

Setup arangodb and node_7.9 and install needed packages in package.json

1. Clone Repo

git clone https://github.com/Irallia/IZW-HU-Parasites.git

2. Download globi's .tsv dump:

wget https://s3.amazonaws.com/globi/snapshot/target/data/tsv/interactions.tsv.gz

Import the extraced tsv-dump with:

arangoimp --file interactions.tsv --type tsv --collection interaction_tsv --create-collection true

• Lydia Buntrock - **

See also the list of contributors who participated in this project.

• Based on https://github.com/majuss/globi-parasites.git.

• give all nodes without ott ids pseudo ids (higher value than all ott ids)
• rebuild the json to graph style (nodes, edges collections) (json and tsv available)
• Plot: number of children per node
• (Presentation)
• tested Tree for cycles -> no cycles

Currently working on:

• write a motivation (in the thesis)

• TMC to parsimony

• add attributes parasitic / freeliving on every leaf node

• Define possible algorithms for calculating node properties.

• Have a look at phylogeny programms: Raxml, mrbayes, beast. (http://evolution.genetics.washington.edu/phylip/software.html#systems)

• run Marius Algorithm on my tree

• Analyse Marius Algorithm (cross evaluation / leave one out evaluation)

In the long run:

• Use / attach / implement an algorithm to give the inner nodes attribute 'parasite' or 'freeliving'. → Find origins for parasitism.
• Attribute aufteilen, parasitismus von vertebraten/...

Future work:

• Add symbiontic or other attributes to the nodes.
• Parsimony analysis of coevolving species associations + recontruction the history of host-parasite associations. Recontruction the history of host-parasite associations.
• enrichment tests. Analyse der Zusammensetzung von Species. Tree über funktionen...
• add Branchlenght: time / DNA / other distances -> DB mit Divergenzzeiten

download Client Tools for Debian 9.0 from https://www.arangodb.com/download-major/debian/

wget https://download.arangodb.com/arangodb32/Debian_9.0/amd64/arangodb3-3.2.3-1_amd64.deb
sudo aptitude update
sudo aptitude upgrade
reboot
sudo dpkg -i arangodb3-3.2.3-1_amd64.deb