Fixed some errors such as indentations and lists that were not able to be indexed.
TIM detects and maps interactions between organisms onto a phylogenetic tree of a target group of organisms.
Interactions are predicted from a species co-occurence-based network (such as one generated by FlashWeave).
TIM assumes that evolutionarily related organisms (refer to as query) interact with evolutionary related organisms (subject) (The reciprocal is not true).
TIM was developed and first applied to infer host group of marine eukaryotic viruses (see references).
TIM tests for enrichement of connection between query and subject at the order level (hard-coded for now).
TIM runs in two main steps:
main.py tree.nwk connections.tsv [ALL, POS, NEG]
downstream.py
- A phylogenetic tree (newick formated) for the
query - A table file containing network connections between
queryandsubjectwith follwing tab separated columns:
Query ID (must be the same as leaves's names in the tree)
Subject ID
Direction of connections (typically the weight, positive or neagtive, in a co-occurence-based network)
P-value (facultative can be NA if you pre-filtred the connections)
Genealogy of the subject ID (Must be NCBI taxonomic terms. If a taxomic name is not found the tool will report it)
Picornavirales.nwk a phylogenetic tree for Picornavirales viruses containing Tara Oceans and reference sequences
connections.txtFlashWeave Inferred associations between Picornavirales and Eukaryotes based on Tara Oceans samples
Results are in the directory myTIMrun
For main.py:
allNodesCounts.txt: Contains count of connections for a given subject and query at a given node.
taxaNotInNCBI.txt : list of taxa's name in your connection file that were not found in the NCBI taxonomy
NODES contains details for ecach visited node.
For downstream.py:
In myTIMrun/downstream:
The two following files belwo can be use to visualize TIM results on ITOL:
PIECHART_ITOL.txt: node with enriched connections towards a group of organism (Q<0.05 by default).
treeWithNodeID_forItolPlot.nwk: the tree you input with node ID added.
| Filename | Description |
|---|---|
main.py |
report number of connections between leaves in the tree and a taxonomic group (NCBI order rank) |
downstream.py |
filters out the output of main.py and prepare files for visualization with iTOL |
filt_form.R |
used by downstream.py for filtering and files formating |
formatForItolPieChart.py |
formats files to plot results on iTOL |
addFeaturesToTreeNode.py |
add node ID to the tree for iTOL visualization |
- Romain Blanc-Mathieu - romain.blancmathieu[@]gmail.com
Blanc-Mathieu R*, Kaneko H*, Endo H, Chaffron S, Hernández-Velázquez R, Nguyen CH, Mamitsuka H, Henry N, Vargas C de, Sullivan MB, et al. 2019. Viruses of the eukaryotic plankton are predicted to increase carbon export efficiency in the global sunlit ocean. bioRxiv:710228. https://www.biorxiv.org/content/10.1101/710228v1.full