FAVITES 1.1.31

• Added ContactNetworkGenerator_DegreeDistribution

FAVITES 1.1.30

• Switched Docker image from Ubuntu 18.04 base to Ubuntu 16.04 base for improved compatibility

FAVITES 1.1.29

• Added Uganda sequences to SeedSequence_Virus

FAVITES 1.1.28

• Added TreeUnit_TruncatedNormal

FAVITES 1.1.27

• Fix Seq-Gen handling of rooted Newick trees with [&R] prefix
• Remove Seq-Gen temporary files after successful execution
• If merged trees exist, only output merged trees (instead of merged + individual trees)
  • Individual trees can trivially be extracted, e.g. using the extract_tree_with function of TreeSwift Tree objects
• Fixed bug in SeedSequence_VirusNonHomYuleHeightGTRGamma and SeedSequence_VirusNonHomYuleHeightGTRGamma
  • Set root edge length of seed tree to 0 so root-to-tip distance exactly seed_tree_height
• Added TreeUnit_Beta
• Added TreeUnit_Dirichlet
• Added TreeUnit_F
• Added TreeUnit_Gumbel
• Added TreeUnit_InverseGaussian
• Added TreeUnit_Logistic
• Added TreeUnit_NoncentralF
• Added TreeUnit_Normal
• Added TreeUnit_Pareto
• Added TreeUnit_Power
• Added TreeUnit_Rayleigh
• Added TreeUnit_Triangular
• Added TreeUnit_Uniform
• Added TreeUnit_Weibull

FAVITES 1.1.26

• Changed VirusYuleHeightGTRGamma to use TreeSAP
• Added SeedSequence_VirusNonHomYuleHeightGTRGamma
• Fixed bug in NodeEvolution_VirusTreeSimulator

NOTE: No Docker image exists for this version because the link to ART was not working at the time of its attempted creation

FAVITES 1.1.25

• Added SeedSequence_VirusYuleHeightGTRGamma

FAVITES 1.1.24

• Added PangeaSim to simulate epidemics modeling HIV in Africa

FAVITES 1.1.23

• Optimized NodeEvolution_VirusTreeSimulator intermediate files
  • VirusTreeSimulator simultaneously opens multiple files per seed individual, which can cause it to be killed on some machines when there is a large number of seed individuals
  • Now, each seed individual is handled one at a time (only ~5 files open per seed individual at a given time)

FAVITES 1.1.22

• Fixed bug in NodeEvolution_VirusTreeSimulator
  • The conversion from FAVITES transmission network to a format supported by VirusTreeSimulator was not properly handling recovery events (u<TAB>u<TAB>t)
• Fixed bug in TimeSample modules that sample from a probabilistic distribution over the infected individual's infection time windows
  • Building the infection windows was not properly handling when a given infected individual did not infect anybody
  • This bug affected TimeSample_Gamma, TimeSample_TruncatedExponential, TimeSample_TruncatedNormal, and TimeSample_Uniform