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