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PATRISTIC specifications

Information


Unique identifier OMICS_33064
Name PATRISTIC
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Mark Gibbs

Additional information


http://www.bioinformatics.org/patristic/manual.html

Publication for PATRISTIC

PATRISTIC citations

 (271)
call_split

Unexpectedly rapid evolution of mandibular shape in hominins

2018
Sci Rep
PMCID: 5943523
PMID: 29743608
DOI: 10.1038/s41598-018-25309-8
call_split See protocol

[…] gle combination including all the three shifts for all n = 3 nodes, plus Brownian motion, which means no shift applied). Alternatively, all selected nodes are partitioned in groups according to their patristic distance, and the number of distinct groups with potential shifts is established via bootstrapped cluster analysis of the internodes distances. This way the number of potential shifts are lo […]

library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] e minimum patristic distance based on dS for each sequence in the single-copy gene trees using the ape package [] in R []. We constructed a Beta distribution from the mean and variance of the minimum patristic dS estimates. We removed any sequence that had a nearest neighbor distance in the 99th percentile of the theoretical Beta distribution from the gene tree and excluded the gene tree from furt […]

library_books

Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites

2018
Nat Commun
PMCID: 5923384
PMID: 29703975
DOI: 10.1038/s41467-018-03923-4

[…] s in branch lengths among paralogous Microsporidia NTTs observed in the Bayesian consensus tree were significant, we used a Bayesian relative rates test. We constructed 95% credible intervals for the patristic distances (that is, the summed branch length differences) from the common ancestor of Microsporidia and Rozella to the tips represented by each NTT that was functionally characterised in thi […]

library_books

Emergence of Vancomycin Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

2018
Sci Rep
PMCID: 5908837
PMID: 29674657
DOI: 10.1038/s41598-018-24614-6

[…] d phylogenetic tree, rooted to the E. faecium DO (TX16) reference genome, was constructed using PhyML (Fig. ). The phylogenetic tree of the VREfm isolates was resolved into five major clades based on patristic distances.Figure 3The largest clade, Phylogenetic Clade 1 (PC1), comprised 47 vanB-harbouring isolates which belonged to ST796 (Fig. ). The ST80 isolates (n = 16) were spread across two sepa […]

call_split

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)

2018
BMC Genomics
PMCID: 5907366
PMID: 29669515
DOI: 10.1186/s12864-018-4650-9
call_split See protocol

[…] moplasy, we conducted saturation plots and posterior predictive analyses. The best-fit CAT+GTR model was selected as a reference for saturation plots. Observed distances (uncorrected P-distances) and patristic distances generated by PATRISTIC [] were then calculated, and the regression from the ordered pairs of distances plotted against each other. The slope of the regression line, indicates the l […]

library_books

The impact of serotype specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan genome

2018
PLoS Pathog
PMCID: 5902063
PMID: 29617440
DOI: 10.1371/journal.ppat.1006966

[…] alignment accessory COGs and antigen variants, ML phylogenies were inferred using RAxML with GTRGAMMA (nucleotide) or GTRCAT (binary) substitution model and 100 bootstrap replicates. The cophenetic (patristic) distances of each phylogeny were read into R, and the meandist function in the package vegan was used to calculate within-group distances for three population groupings: serogroup, serotype […]

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PATRISTIC institution(s)
School of Botany and Zoology, The Australian National University, Canberra, ACT, Australia

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