scholarly journals Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions

2015 ◽  
Vol 32 (8) ◽  
pp. 2208-2216 ◽  
Author(s):  
Stefan Zoller ◽  
Veronika Boskova ◽  
Maria Anisimova
Keyword(s):  
Maximum Likelihood ◽  
Codon Substitution ◽  
Maximum Likelihood Tree ◽  
Substitution Models ◽  
Tree Estimation

scholarly journals CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

2013 ◽  
Vol 30 (6) ◽  
pp. 1270-1280 ◽  
Author(s):  
Manuel Gil ◽  
Marcelo Serrano Zanetti ◽  
Stefan Zoller ◽  
Maria Anisimova
Keyword(s):  
Maximum Likelihood ◽  
Codon Substitution ◽  
Substitution Models ◽  
Phylogeny Estimation ◽  
Maximum Likelihood Phylogeny

scholarly journals Bayesian Comparisons of Codon Substitution Models

Genetics ◽  
2008 ◽  
Vol 180 (3) ◽  
pp. 1579-1591 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Nicolas Lartillot ◽  
Hervé Philippe
Keyword(s):  
Codon Substitution ◽  
Substitution Models

scholarly journals Application of PCR-DGGE method for identification of nematode communities in pepper growing soil

2016 ◽  
Vol 7 (1) ◽  
pp. 9-14
Author(s):  
Duong Duc Hieu
Keyword(s):  
Maximum Likelihood ◽  
Community Sample ◽  
Nematode Species ◽  
Viet Nam ◽  
Soil Nematode ◽  
Nematode Communities ◽  
Maximum Likelihood Tree ◽  
Relationship Of ◽  
First Time ◽  
Soil Nematode Communities

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysisoffive soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

A contribution towards the systematics of Magneuptychia Forster, 1964: Caeruleuptychia francisca (Butler, 1870), n. comb. (Lepidoptera: Nymphalidae: Satyrinae)

2020 ◽  
pp. 1-11
Author(s):  
Shinichi Nakahara ◽  
Kaylin Kleckner ◽  
Gerardo Lamas ◽  
Blanca Huertas ◽  
Keith R. Willmott
Keyword(s):  
Maximum Likelihood ◽  
Molecular Data ◽  
Maximum Likelihood Analysis ◽  
Maximum Likelihood Tree ◽  
Likelihood Analysis ◽  
First Time

We here transfer an euptychiine taxon hitherto placed in the polyphyletic genus Magneuptychia Forster, 1964, to Caeruleuptychia Forster, 1964. Caeruleuptychia francisca (Butler, 1870), n. comb. is reclassified based on a morphology-based maximum likelihood analysis, which is consistent with ongoing analyses of molecular data. Two putative synapomorphic characters are identified for the “Caeruleuptychia umbrosa clade”, one of which appears to be an unusual characteristic of euptychiine butterflies and is tested by optimizing onto the maximum likelihood tree. We also discuss the systematic placement of three additional enigmatic Caeruleuptychia species. A lectotype is designated for Euptychia francisca, and the genitalia of this species are illustrated here for the first time.

Morphology and molecular analysis ofOncicola venezuelensis(Acanthocephala: Oligacanthorhynchidae) from the ocelotLeopardus pardalisin Brazil

2016 ◽  
Vol 91 (5) ◽  
pp. 605-612 ◽  
Author(s):  
E.G.N. Santos ◽  
M. Chame ◽  
V.A. Chagas-Moutinho ◽  
C.P. Santos
Keyword(s):  
Maximum Likelihood ◽  
Genetic Analysis ◽  
National Park ◽  
Genetic Data ◽  
Genetic Profile ◽  
28S Rrna ◽  
Leopardus Pardalis ◽  
Ultrastructural Studies ◽  
Maximum Likelihood Tree ◽  
Geographical Locality

AbstractOncicola venezuelensisMarteau, 1977 was found parasitizing adults ofLeopardus pardalis(Linnaeus) found dead in Serra da Capivara National Park, Piauí state, Brazil, a new geographical locality reported for the species. The diversity ofOncicolaTravassos, 1916 species is large, but genetic data are scarce. This article presents the results of genetic, morphological and ultrastructural studies carried out for taxonomic purposes. The first ultrastructural view showed a globular, short proboscis with 36 hooks, divided into six longitudinal rows of six hooks each. Hooks differ in size and shape: hooks I, II and III have a ‘chisel-shaped’ tip. The genetic profile included new sequences of ribosomal DNA ITS1, 5.8S and ITS2, and partial 28S rRNA regions. The results of maximum-likelihood tree analyses for each region showed Oligacanthorhynchidae Southwell et Macfie, 1925 close to Gigantorhynchidae Hamann, 1892 (supported >91%). Both use mammals and birds as definitive hosts. Morphological and ultrastructural studies combined with genetic analysis shed more light on the diversity ofOncicolaspecies.

Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates

2005 ◽  
Vol 12 (9) ◽  
pp. 1166-1182 ◽  
Author(s):  
Ole F. Christensen ◽  
Asger Hobolth ◽  
Jens L. Jensen
Keyword(s):  
Codon Substitution ◽  
Pseudo Likelihood ◽  
Likelihood Analysis ◽  
Substitution Models

Codon substitution models based on residue similarity and their applications

Gene ◽  
2012 ◽  
Vol 509 (1) ◽  
pp. 136-141 ◽  
Author(s):  
Xinsheng Liu ◽  
Hui Liu ◽  
Wanlin Guo ◽  
Keming Yu
Keyword(s):  
Codon Substitution ◽  
Substitution Models

scholarly journals ADOPS - Automatic Detection Of Positively Selected Sites

2012 ◽  
Vol 9 (3) ◽  
pp. 18-32 ◽  
Author(s):  
David Reboiro-Jato ◽  
Miguel Reboiro-Jato ◽  
Florentino Fdez-Riverola ◽  
Cristina P. Vieira ◽  
Nuno A. Fonseca ◽  
...  
Keyword(s):  
Amino Acid ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Sequence Data ◽  
Automatic Detection ◽  
Acid Sites ◽  
Nucleotide Sequence Data ◽  
Software Applications ◽  
Codon Substitution ◽  
Positively Selected Sites

Summary Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.

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