Phylogenetic Inference: Linear Invariants and Maximum Likelihood

Biometrics ◽  
1993 ◽  
Vol 49 (2) ◽  
pp. 543 ◽  
Author(s):  
W. C. Navidi ◽  
G. A. Churchill ◽  
A. von Haeseler
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Inference ◽  
Linear Invariants

scholarly journals PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W557-W559 ◽  
Author(s):  
S. Guindon ◽  
F. Lethiec ◽  
P. Duroux ◽  
O. Gascuel
Keyword(s):  
Maximum Likelihood ◽  
Web Server ◽  
Phylogenetic Inference

scholarly journals New Fusarium species from the Kruger National Park, South Africa

MycoKeys ◽  
2018 ◽  
Vol 34 ◽  
pp. 63-92 ◽  
Author(s):  
Marcelo Sandoval-Denis ◽  
Wijnand J. Swart ◽  
Pedro W. Crous
Keyword(s):  
South Africa ◽  
Maximum Likelihood ◽  
New Taxa ◽  
National Park ◽  
Fusarium Species ◽  
Phylogenetic Inference ◽  
Kruger National Park ◽  
Bayesian Approaches ◽  
Molecular Analyses ◽  
Species Complexes

Three new Fusarium species, F.convolutans, F.fredkrugeri, and F.transvaalense (Ascomycota, Hypocreales, Nectriaceae) are described from soils collected in a catena landscape on a research supersite in the Kruger National Park, South Africa. The new taxa, isolated from the rhizosphere of three African herbaceous plants, Kyphocarpaangustifolia, Melhaniaacuminata, and Sidacordifolia, are described and illustrated by means of morphological and multilocus molecular analyses based on sequences from five DNA loci (CAL, EF-1 α, RPB1, RPB2 and TUB). According to phylogenetic inference based on Maximum-likelihood and Bayesian approaches, the newly discovered species are distributed in the Fusariumbuharicum, F.fujikuroi, and F.sambucinum species complexes.

scholarly journals Two C++ Libraries for Counting Trees on a Phylogenetic Terrace

2017 ◽  
Author(s):  
R. Biczok ◽  
P. Bozsoky ◽  
P. Eisenmann ◽  
J. Ernst ◽  
T. Ribizel ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Phylogenetic Inference ◽  
Source Codes ◽  
Likelihood Score ◽  
Order Of Magnitude ◽  
Tree Topologies ◽  
Tree Space ◽  
Bayesian Phylogenetic Inference ◽  
Counting Trees

AbstractMotivationThe presence of terraces in phylogenetic tree space, that is, a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al, (2011). However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the unavailability of an efficient library implementation to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace, and (iii) enumerate all trees on a terrace.ResultsIn our bioinformatics programming practical we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating the trees on a terrace. Both implementations yield exactly the same results and are more than one order of magnitude faster and require one order of magnitude less memory than a previous 3rd party python implementation.AvailabilityThe source codes are available under GNU GPL at https://github.com/[email protected]

scholarly journals IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

2020 ◽  
Vol 37 (5) ◽  
pp. 1530-1534 ◽  
Author(s):  
Bui Quang Minh ◽  
Heiko A Schmidt ◽  
Olga Chernomor ◽  
Dominik Schrempf ◽  
Michael D Woodhams ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Software Package ◽  
Genomic Data ◽  
Phylogenetic Inference ◽  
Sequence Evolution ◽  
Computational Approaches ◽  
New Models ◽  
User Friendly

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

Phylogeny of Anatolian (Turkey) species in the Digitalis sect. Globiflorae (Plantaginaceae)

Phytotaxa ◽  
2016 ◽  
Vol 244 (3) ◽  
pp. 263 ◽  
Author(s):  
İsmail Eker ◽  
Buhara Yücesan ◽  
Muhammad Sameeullah ◽  
Walter Welß ◽  
Frieder Müller-Uri ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Genetic Marker ◽  
Plant Species ◽  
Phylogenetic Inference ◽  
Distinct Species ◽  
Neighbor Joining ◽  
Flora Of Turkey ◽  
Cdna Sequences ◽  
Likelihood Model ◽  
Important Enzyme

This study analyses phylogenetic and morphological relationships regarding the taxonomy of Digitalis sect. Globiflorae. Progesterone 5β-reductase (P5βR) is an important enzyme for cardenolide biosynthesis as well as a novel genetic marker inferring phylogenetic and biogeographic relationships in many plant species. Phylogenetic inference was conducted using the neighbor-joining method and maximum likelihood model on cDNA sequences of highly conserved P5βR (97.0–99.6%) isolated from members of sect. Globiflorae, including Digitalis trojana, D. cariensis, D. lamarckii, D. lanata subsp. lanata, D. ferruginea subsp. ferruginea and D. ferruginea subsp. schischkinii. Our phylogenetic and morphological results largely support Davis’ system of the genus Digitalis in the Flora of Turkey. We propose the existence of four species and three subspecies in sect. Globiflorae for Turkey. Digitalis cariensis is a distinct species endemic to Turkey. In spite of high morphological similarities, D. lamarckii was separated from D. trojana and D. lanata. Digitalis trojana is accepted at the infraspecific rank as D. lanata subsp. trojana. In addition, D. ferruginea is ranked under the two subspecies following Werner’s treatment. Our study presents a new understanding of the speciation patterns of endemic and non-endemic eastern Digitalis species distributed in Anatolia, Turkey, underlying molecular, biogeographical and comparative morphological analyses.

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