dschrempf / geneclocks

Geneclocks project

Geneclocks project

For now, only simulation of reconstructed trees is supported.

Installation

1. Install Stack.

2. Clone this project.

    git clone https://github.com/dschrempf/geneclocks
   

3. Build.

    cd geneclocks
    stack build
   

4. Run simulate-trees. For instance, read the help message.

   stack exec simulate-trees -- -h
   
   --
   
   Simulate reconstructed trees
   
   Usage: simulate-trees [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE]
                         [-l|--lambda DOUBLE] [-m|--mu DOUBLE]
                         [-s|--summary-statistics] [-v|--verbosity] [-q|--quiet]
     Simulate reconstructed trees using the point process. See Gernhard, T. (2008).
     The conditioned reconstructed process. Journal of Theoretical Biology, 253(4),
     769–778. http://doi.org/10.1016/j.jtbi.2008.04.005
   
   Available options:
     -h,--help                Show this help text
     -t,--nTrees INT          Number of trees (default: 10)
     -n,--nLeaves INT         Number of leaves per tree (default: 5)
     -H,--height DOUBLE       Fix tree height (no default)
     -l,--lambda DOUBLE       Birth rate lambda (default: 1.0)
     -m,--mu DOUBLE           Death rate mu (default: 0.9)
     -s,--summary-statistics  Only output number of children for each branch
     -v,--verbosity           Verbosity
     -q,--quiet               Be quiet
   
   If no tree height is given, the heights will be randomly drawn from the expected
   distribution given the number of leaves, the birth and the death rate.
   

   Or do a test simulation.

   stack exec simulate-trees
   
   --
   
   Reconstructed trees simulator version 0.1.0.0.
   Command line: simulate-trees 
   
   -- Arguments
   Number of simulated trees: 10
   Number of species per tree: 5
   Height of trees: 1.0
   Birth rate: 1.0
   Death rate: 0.9
   Verbosity: False
   Quiet: False
   
   -- Simulation
   (0:0.3774855500765698,((1:2.0154241024089484e-2,2:2.0154241024089484e-2)0:0.2194498304554361,(3:0.18875196496260377,4:0.18875196496260377)0:5.085210651692179e-2)0:0.13788147859704425)0:0.6225144499234302;
   ((0:0.5177388882792351,1:0.5177388882792351)0:0.17579988502229682,((2:2.4071319480028328e-3,3:2.4071319480028328e-3)0:0.5087754559038138,4:0.5111825878518166)0:0.18235618544971532)0:0.3064612266984681;
   (0:0.5844174857147952,(1:0.5698359606751093,(2:0.4090026429825453,(3:9.963595012789103e-2,4:9.963595012789103e-2)0:0.30936669285465423)0:0.16083331769256404)0:1.4581525039685905e-2)0:0.41558251428520476;
   (0:0.45748809145221386,((1:3.1144304318300375e-3,2:3.1144304318300375e-3)0:0.27978666828928417,(3:5.2227265132491034e-2,4:5.2227265132491034e-2)0:0.23067383358862315)0:0.17458699273109968)0:0.5425119085477861;
   (((0:6.735311917877203e-2,1:6.735311917877203e-2)0:3.0393396323536895e-2,(2:7.177846060176821e-2,3:7.177846060176821e-2)0:2.5968054900540716e-2)0:0.13914199440844016,4:0.23688850991074908)0:0.7631114900892509;
   ((0:0.2100809945775664,(1:0.15777006486332162,2:0.15777006486332162)0:5.231092971424478e-2)0:3.0252921468290034e-2,(3:0.1501753882670414,4:0.1501753882670414)0:9.015852777881503e-2)0:0.7596660839541436;
   ((((0:3.2439737590665e-2,1:3.2439737590665e-2)0:0.36980767383515173,2:0.4022474114258167)0:6.58267022258962e-2,3:0.4680741136517129)0:0.40516374800937494,4:0.8732378616610879)0:0.12676213833891214;
   ((((0:0.11196444537163554,1:0.11196444537163554)0:5.056354677189623e-3,2:0.11702080004882516)0:0.28450453494869715,3:0.4015253349975223)0:2.0093485295044233e-2,4:0.42161882029256653)0:0.5783811797074334;
   (0:0.9803439102203049,(((1:4.690857183501333e-2,2:4.690857183501333e-2)0:3.103274247509455e-2,3:7.794131431010788e-2)0:0.5342528598722517,4:0.6121941741823596)0:0.3681497360379453)0:1.965608977969513e-2;
   ((0:0.3170383445505747,1:0.3170383445505747)0:0.40209444148245527,((2:0.1770647724894815,3:0.1770647724894815)0:0.4894164144749219,4:0.6664811869644034)0:5.26515990686266e-2)0:0.28086721396697;
   

   You can also use quiet mode (only print simulated trees).

   stack exec simulate-trees -- -q
   
   --
   
   ((0:0.68534719435169,1:0.68534719435169)0:0.21528252085106026,(2:0.3609135961613327,(3:0.22004788342525208,4:0.22004788342525208)0:0.1408657127360806)0:0.5397161190414176)0:9.937028479724974e-2;
   ((0:0.5436590952526373,1:0.5436590952526373)0:0.10984879686076143,((2:0.3646311967978449,3:0.3646311967978449)0:0.1502264583081801,4:0.514857655106025)0:0.13865023700737378)0:0.34649210788660123;
   (((0:0.3008707041549576,(1:0.271374763205572,2:0.271374763205572)0:2.949594094938557e-2)0:2.8234253178400948e-2,3:0.32910495733335854)0:5.8409296357698426e-2,4:0.38751425369105696)0:0.612485746308943;
   (((0:3.74908528727916e-2,(1:1.3349768604509465e-2,2:1.3349768604509465e-2)0:2.4141084268282136e-2)0:1.915156490140029e-2,3:5.664241777419189e-2)0:5.6816091240475486e-2,4:0.11345850901466738)0:0.8865414909853326;
   ((0:5.442608353607999e-2,(1:3.155629285750777e-2,2:3.155629285750777e-2)0:2.286979067857222e-2)0:0.7517814558302057,(3:0.14172123866053613,4:0.14172123866053613)0:0.6644863007057497)0:0.19379246063371425;
   (((0:0.41327220897168615,1:0.41327220897168615)0:0.11338569839383617,(2:0.3029320951884167,3:0.3029320951884167)0:0.22372581217710563)0:0.16023726627105084,4:0.6868951736365732)0:0.31310482636342685;
   (0:0.7524695865441795,((1:0.4856958670853718,2:0.4856958670853718)0:0.19805060662336038,(3:9.289763476186218e-2,4:9.289763476186218e-2)0:0.59084883894687)0:6.87231128354473e-2)0:0.2475304134558205;
   ((0:0.3118323950570037,1:0.3118323950570037)0:0.5344516596304831,((2:0.37152779665907054,3:0.37152779665907054)0:1.1784860724386448e-3,4:0.3727062827315092)0:0.4735777719559776)0:0.1537159453125132;
   (0:0.5527626238311962,(1:0.34894677621430875,((2:1.2708873676922612e-2,3:1.2708873676922612e-2)0:0.24866670306415153,4:0.26137557674107414)0:8.75711994732346e-2)0:0.20381584761688748)0:0.44723737616880377;
   ((0:0.12476268814676579,1:0.12476268814676579)0:0.5616208523887856,((2:0.28734210014844747,3:0.28734210014844747)0:0.3197180138417644,4:0.6070601139902119)0:7.932342654533953e-2)0:0.3136164594644486;
   
   

5. Install (take care that the binary is installed into your PATH).

    stack install geneclocks:\exe:\simulate-trees