DIMSIM-data

SARS-Cov2 experiments

COVID/setup/*

Python script to generate parameters (arguments.txt) for each replicate of COVID simulations

COVID/simulator/*

arguments.txt

One example of input parameters for the simulator

kemrFreq.txt

Our 5-mer model; Yaari's 5-mer model is kmerFreq_yaari.txt

simulator.hpp

Our evolution model

main.cpp

Our driver code defining the flu simulation

simulator

Binary compiled with command g++ -std=c++11 -O3 main.cpp -o simulator

COVID/reconstruction_tools/*

Reconstruction tools and helper scripts we implemented

COVID/tree/real/*.sh

Shell scripts to run reconstruction methods

COVID/tree/real/[replicate]/[samplesize]/*

Reconstructed trees in raw format

dnapars: RAxML_MajorityRuleExtendedConsensusTree.dnapars_greedy and RAxML_MajorityRuleConsensusTree.dnapars_consensus

beast: beast.nexus

raxml: RAxML_bestTree.raxml-with-root

igphyml: seq_with_root.fasta_igphyml_tree_igphyml.txt

gctree: gctree.nw

immunitree: immunitree.txt

mst: mst.result

COVID/output/[replicate]/[samplesize]/*

Simulated and reconstructed trees in the following format:

[#labels]
[#branches]
[root]
[label_1 node_1]
[label_2 node_2]
...
[parent_1 child_1]
[parent_2 child_2]
...

COVID/metric/*

Evaluation metrics and scripts to help formating trees to the format above

COVID/stat/*

Figures in the paper along with scripts and data to reproduce those figures

Simulated sequences

See here.

Flu experiments

stat/*