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Physher specifications


Unique identifier OMICS_12356
Name Physher
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Physher requires a single configuration file. For inferring rates and times, the configuration file requires an alignment (FASTA or NEXUS format) and a rooted tree (Newick or NEXUS format).
Output data Output trees are in nexus format as they contain information such as rates and confidence intervals.
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Mathieu Fourment

Publication for Physher

Physher citations


The impact of migratory flyways on the spread of avian influenza virus in North America

BMC Evol Biol
PMCID: 5445350
PMID: 28545432
DOI: 10.1186/s12862-017-0965-4

[…] Migration rates of avian influenza viruses between discrete geographic locations were analysed using a reversible continuous-time Markov chain model as described in Pagel [] and implemented in Physher []. The state space of the Markov chain was defined as the set of geographic locations. For the phylogeographic analysis of each gene segment, we fixed the tree topology and the branch lengths […]


Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry

BMC Evol Biol
PMCID: 4481119
PMID: 26111936
DOI: 10.1186/s12862-015-0410-5
call_split See protocol

[…] Phylogenetic trees were inferred using maximum likelihood available in Physher [] employing the generalised time-reversible (GTR) substitution model and a discretised gamma distribution (4 categories) of rates across sites (Γ4). Using the year of isolation as sampling ti […]

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Physher institution(s)
Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia

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