Clockwork Evolver


Clockwork Evolver is tool for simulating tree-like molecular evolution. It starts with a single ancestoral DNA sequence, and produces a specified number of current day sequences. It only uses substitutions, not indels nor recombinations. The main output a multiple alignment of generated sequences, in FASTA format, written to standard output. (This means it can be piped into next command, or saved into a file using >FILE). In addition, it can optionally save the correct tree (rooted tree, unrooted tree, or both).

This tool assumes molecular clock, which means that substitution rate is constant for all branches of the tree and during the entire simulated time.

This tool is useful for benchmarking phylogeny reconstruction methods. That is, a phylogeny can be inferred from aligned sequences (with or without involving the step of making a distance matrix). This phylogeny can be then compared with the correct one, to measure accuracy of the reconstruction.


Installing and using

It's a perl script. It can be executed using command like: --n 10 --length 1000 --sps 0.2 --out-unrooted-tree 10.newick >10.fa

On Windows you may need to install Perl (e.g., Strawberry Perl), and prepend "perl " to this command.


--n N - Produce N sequences.

--length L - Produce sequences of L bp.

--sps R - Generate R substitutions per site (over the simulated time span).

--out-rooted-tree FILE - Save the correct rooted tree into FILE, in Newick format.

--out-unrooted-tree FILE - Save the correct unrooted tree into FILE, in Newick format.