Fastdating info

23 Nov

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LSD: LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES FROM SERIAL PHYLOGENIES - v0.2 by Thu-Hien TO If you use this software, please cite: “ Fast dating using least-squares criteria and algorithms”, T-H. Some examples: 1) Examples of command line: for rooted tree, constrained mode, and using variances ./lsd -i rootedtree_file -d date_file -c -v for rooted tree, constrained mode, re-estimate the root position around the given root, and non variances ./lsd -i rootedtree_file -d date_file -c -r l for unrooted tree without outgroups, without constraints, estimate the root position, and using variances ./lsd -i unrootedtree_file -d date_file -c -v -r a for unrooted tree with outgroups, constrained mode, using varainces, remove outgroups to obtain the root ./lsd -i unrootedtree_file -d date_file -g outgroup_file -c -v for rooted tree, constrained mode, using variances, and using given rates to estimate dates ./lsd -i rootedtree_file -d date_file -w given_rate_file -c -v for rooted tree, estimating relative dates with date root=0 and date of all leaves=1, using variances, with constraint ./lsd -i tree_file -c -v -a 0 -z 1 2) Examples of input files: Example of Input_tree_file format (newick) (a:0.12,(b:0.3,c:0.5):0.4); ((a:0.12,b:0.3):0.7,c:0.5); Example of Input_date_file format: 3 a 1999 b 2000 c 1780 Example of Outgroup_file format: 2 outgroup1 outgroup2 Example of given_rate_file format: 0.0068 0.0052 3) Output files: .result : contain the estimated rate, root date and the value of the log likelihood function if variances are used.

If the program is installed or the path of the executable file is added into PATH, you can run it from anywhere by typing lsd (and with or without options).

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