updating scrm for repeats
Use Newick form to express local genealogies, and save into a tree file. Modified the log option
oops... manual was complaining, fixed ...
consider only copy the local tree
setting up member of node class, in order to apply felsenstein's pruning algorithm
modify likelihood, and functions for copying forests
edited copy_forest.cc, will switch to branch copy-forest
edited copy forest, should ve checkout branch copyforest first ...
disable some of the debugging messages
added packages needed for building scrm
formated bash commands
generate segregating sites, convert the output gene tree branch length to 4Ne
using vector instead of valarray for identify the descndnt
tidy up the output file
working progress, need to revise the function to write trees and simulate segregating sites data, node containers contain internal nodes that are not necessary for the newick representation, should skip them, function should split into cases, for local nonlocal nodes, local nodes: internal nodes, tip nodes; internal nodes: cusual for the newick format, or not necessary; tip nodes: actual tip nodes, or tip nodes that is not local, (should draw a venn diagram first to think about the cases) ... for segregating site, only focus on the local tree nodes, verify the branches above internal nodes do not make difference when simulation is undertaken
correct rate for waiting time (along sequence) for the new recombination event to occur, sequence is not limited in the unit interval, this will be changed if the number of sites is specified, in which case, it should work within a unit interval
making corrections for outputting the newick formatted tree strings, use interger for sites?
making corrections for outputting the newick formatted tree strings, use interger for sites?
Merge branch 'master' of https://github.com/paulstaab/scrm
correction for copy forest