Usage

Inputs

Rules

1. Sequence names in the alignment and tree files must match.
2. Sequence names cannot contain these characters ,[]():;
3. Sequences contain the time of sampling at the end of their names and the date should start with an underscore (e.g. seq1_2010.5). Sequences are assumed to be isochronous if dates are not present.
4. No duplicate sequence names.
5. The tag for calibration points for an internal node inside a tree should be: [&cal_height={10,15}].
6. Calibration points are only for isochronous sequences (for now).
7. NEXUS files:

• Names can contain spaces but the whole name has to be surrounded by quotes (e.g. "seq 1_2001.3")
• Keep the file simple.

Alignment

>seq1_2001.3
AAAAAAAA
>seq2_2011.3
AAAAAAAT
>seq3_2013.72
AAAAAAAG
>seq4_2008.2
AAAAAAAC

or

#NEXUS
begin data;
seq1_2001.3    AATCTCGA
seq2_2011.3    AAACTCGA
seq3_2013.72   AATTTCGA
seq4_2008.2    AATTTCGG
end;

Tree

(((seq1_2001.3, seq2_2011.3), seq3_2013.72), seq4_2008.2);

or

#NEXUS
begin trees;
(((seq1_2001.3, seq2_2011.3), seq3_2013.72), seq4_2008.2);
end;

Configuration file

physher expects a configuration file as argument.

Each line of the configuration file is of the form: key=value

Example:

input.sequences = fluA.fa
input.tree      = fluA.tree
output.stem     = fluA
substmodel.type = HKY
clock           = strict

Command line

Alternatively, physher can be run from the command line:

./physher -m HKY -i fluA.fa -t fluA.tree -C strict -o fluA

Inputs/outputs

Option	Key	Type	Value	Default	Note
-i	input.sequences	string	path to sequence file	Mandatory	sequence file in FASTA or NEXUS format
-t	input.tree	string	path to rooted tree file	Mandatory	tree file in newick or NEXUS format
-o	output.stem	string	outptut file name	input.sequences

Substitution model

Option	Key	Type	Value	Default	Note
-m	substmodel.type	string	GTR, HKY, K80, JC69, or GY94	Mandatory	00000, 00001,...,01234 can also be used
-r	substmodel.kappa	real	value > 0	empirical	Only for HKY, K80, and GY94
-r	substmodel.rates	array of real	values > 0	empirical	Nucleotide only. For GTR it could be: 0.1,0.1,0.2,0.6,0.9
	substmodel.rates.fixed	boolean	true or false	false	Fixed to values specified in substmodel.rates
-f	substmodel.freqs	array of real	0 < values < 1	empirical	Nucleotide model only. e.g. 0.1,0.2,0.3,0.4
	substmodel.freqs.fixed	boolean	true or false	false	Fixed to values specified in substmodel.freqs
	substmodel.codon.omega	real	value > 0	1	GY94 only
	substmodel.heterogeneity	string	no, gamma, inv, or gammainv	no
-c	substmodel.heterogeneity.gamma.cat	integer	value > 0	4	Number of rate categories
-a	substmodel.heterogeneity.gamma.alpha	real	value > 0	0.3	Parameter of gamma distribution
	substmodel.heterogeneity.gamma.alpha.fixed	boolean	true or false	false	Fixed to value specified in substmodel.heterogeneity.gamma.alpha
	substmodel.heterogeneity.pinv	real	0 < value < 1	0.5	proportion of invariant sites

Clock

Option	Key	Type	Value	Default	Note
-C	clock	string	strict, local, or discrete		If not set, no clock is assumed
-S	clock.algorithm	string	ga or greedy		ga (local and discrete clocks) greedy (local clock only)
--forward	clock.forward	bool	true or false	true	Time is forward if a large number = present and smaller number = past
--rate	clock.rate	integer	value > 0		It is not fixed, it is just a guess for a better start

Genetic algorithm

Option	Key	Type	Value	Default	Note
--ga-pop	ga.popsize	integer	value > 0	30
--ga-gen	ga.ngen	integer	value > 0	200
--ga-no-improv	ga.maxnoimprovement	integer	value > 0	50

Bootstrap

Option	Key	Type	Value	Default	Note
-b	bootstrap	integer	value >= 0	0
--b-threads	bootstrap.threads	integer	value > 0	10

Miscelleneous

Option	Key	Type	Value	Default	Note
-R	random.seed	integer	value >= 0	random number
-T	nthreads	integer	value > 0	10	Number of threads used by GA and greedy algorithm
--gc	sequences.geneticcode	integer	0 <= value <= 14	0	Only for codon models. See genetic code [Inputfile#Genetic_codes section]
--ic	ic	string	AIC, AICc, or BIC	AICc	For greedy and genetic algorithms

Genetic codes

Value	Type
0	Universal
1	Vertebrate Mitochondrial
2	Yeast
3	Mold Protozoan Mitochondrial
4	Mycoplasma
5	nvertebrate Mitochondrial
6	Ciliate
7	Echinoderm Mitochondrial
8	Euplotid Nuclear
9	Bacterial
10	Alternative Yeast
11	Ascidian Mitochondrial
12	Flatworm Mitochondrial
13	Blepharisma Nuclear
14	No stops