Update readme

README.md

@@ -2,13 +2,16 @@ Copy Number Evolutionary Tree Analysis
 =============
 
 # Introduction
-This repository contains a set of programs to simulate and build phylogenetic trees from copy number alterations (CNAs) in tumour genomes from multiple samples of a patient.
+This repository contains a set of programs to simulate and build phylogenetic trees from copy number alterations (CNAs) detected from whole genome sequencing of multiple samples of a patient.
 
 There are mainly 3 programs:
 * cnets: simulating CNAs along a phylogenetic (coalescence) tree
-* cnetml: building phylogenetic trees from copy numbers with maximum likelihood approach
+* cnetml: building phylogenetic trees from copy numbers with maximum likelihood approach, capable of jointly inferring the tree topoloy, node ages, and muation rates from total copy number of longitudinal samples
 * cnetmcmc (still under development): building phylogenetic trees from copy numbers with Bayesian MCMC approach
 
+The first two programs are described in the paper:
+- [Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples. bioRxiv. 2022 Mar 20:2022-03.](https://www.biorxiv.org/content/10.1101/2022.03.18.484889v1)
+
 
 # Installation
 This package is mostly written in C++. There are a few scripts written in R and Python, for plotting and text processing.
@@ -187,7 +190,7 @@ For whole genome doubling, chr is assigned to 0 and seg_ID is assigned to -1.
 
 # Tree building with cnetml
 
-cnetml is a new maximum likelihood method based on a novel evolutionary model of CNAs to infer phylogenies from spatio-temporal samples taken within a single patient. 
+cnetml is a new maximum likelihood method based on a novel evolutionary model of CNAs to infer phylogenies from multiple samples taken within a single patient. 
 
 
 There are 4 running modes in cnetml.

code/cnetml.cpp

@@ -1131,8 +1131,8 @@ int main(int argc, char** const argv){
 
     // mutation rates
     ("mu,x", po::value<double>(&mu)->default_value(0.02), "overall mutation rate")
-    ("dup_rate", po::value<double>(&dup_rate)->default_value(0.01), "duplication rate")
-    ("del_rate", po::value<double>(&del_rate)->default_value(0.01), "deletion rate")
+    ("dup_rate", po::value<double>(&dup_rate)->default_value(0.001), "duplication rate")
+    ("del_rate", po::value<double>(&del_rate)->default_value(0.001), "deletion rate")
     ("chr_gain_rate", po::value<double>(&chr_gain_rate)->default_value(0), "chromosome gain rate")
     ("chr_loss_rate", po::value<double>(&chr_loss_rate)->default_value(0), "chromosome loss rate")
     ("wgd_rate", po::value<double>(&wgd_rate)->default_value(0), "WGD (whole genome doubling) rate")

code/common.hpp

@@ -51,7 +51,7 @@ const int WGD_CUTOFF = 3;    // genome ploidy to determine WGD
 // key: chr, seg, copy_number
 typedef map<int, map<int, int>> copy_number;
 
-const string VERSION = "0.1";
+const string VERSION = "1.0";
 
 
 // read-only