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63 results for “maximum parsimony”
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West) in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West)
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae) in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae)
Fig. 2. Maximum parsimony tree inferred from 18S in Novel piroplasmid and Hepatozoon organisms infecting the wildlife of two regions of the Brazilian Amazon
Fig. 2. Maximum parsimony tree inferred from 18S rRNA gene sequences of Hepatozoon spp., with Babesia sp. as outgroup (488 characters; 52 parsimony-informative sites). Numbers at nodes are the support values for the major branches (bootstrap over 500 replicates). The sequences obtained in this study are in bold. Numbers in brackets are GenBank accession numbers.
Fig. 1. Maximum parsimony tree inferred from 18S in Novel piroplasmid and Hepatozoon organisms infecting the wildlife of two regions of the Brazilian Amazon
Fig. 1. Maximum parsimony tree inferred from 18S rRNA gene sequences of piroplasmids (Babesia spp., Theileria spp., Cytauxzoon spp.), with Plasmodium ovale as outgroup (316 characters; 65 parsimony-informative sites). Numbers at nodes are the support values for the major branches (bootstrap over 500 replicates). The sequences obtained in this study are in bold. Numbers in brackets are GenBank accession numbers.
Fig. 4. Maximum Parsimony consensus tree for the mitochondrial gene Cytochrome Oxidase I in New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae) with comments on the Moenkhausia oligolepis species complex
Fig. 4. Maximum Parsimony consensus tree for the mitochondrial gene Cytochrome Oxidase I. Numbers represent values of 1000 bootstrap replicates.
Fig. 4. Unrooted maximum parsimony cox1 in How many species of whipworms do we share? Whipworms from man and other primates form two phylogenetic lineages
Fig. 4. Unrooted maximum parsimony cox1 tree of the genus Trichuris Roederer, 1761 as inferred from partial cox1 amino acid se- quences. Numbers above branches indicate MP bootstrap support (1 000 replicates)/ML bootstrap support (1 000 replicates)/NJ bootstrap support (1 000 replicates). Sequences newly reported in this study are bold typed.
Figure 2. - Bayesian (GTR+Γ+I and HKY+Γ models) and maximum likelihood 50% majority-rule consensus tree. Numbers in the nodes represent posterior probabilities (GTR+Γ+I and HKY+Γ, respectively), and bootstrap value for maximum likelihood and parsimony analyses, respectively. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas. MYBP–million years before present.
Figure 2. - Bayesian (GTR+Γ+I and HKY+Γ models) and maximum likelihood 50% majority-rule consensus tree. Numbers in the nodes represent posterior probabilities (GTR+Γ+I and HKY+Γ, respectively), and bootstrap value for maximum likelihood and parsimony analyses, respectively. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas. MYBP–million years before present.
Supplementary Data: MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation
<p>Supplementary Data<br> MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation<br> Submitted to BMC Evolutionary Biology</p> <p>This record contains PANDIT based dataset and TreeBASE dataset (Nguyen et al. 2015) which are analyzed by different bootstrap methods in the study "MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation". The PANDIT based dataset (compressed in file data_pandit.tar.gz) is used to benchmark the accuracy of bootstrap estimates. The TreeBASE dataset (compressed in file data_treebase.tar.gz) is used to benchmark computing times and capability of finding the best-known MP scores. </p> <p>After being uncompressed, the PANDIT based dataset comprises two subdirectories corresponding to the simulated DNA and AA MSAs. They were generated by Seq-Gen (Rambaut and Grass 1997), where the model parameters and true tree were inferred from the original MSAs downloaded from the PANDIT database (Whelan et al. 2006).</p> <ul> <li>Inside "dna" subdirectory, there are 6,207 numbered directories corresponding to 6,207 DNA MSAs. Note that the numbering of these directories is not consecutive because we excluded MSAs where TNT or PAUP* runs did not finish. In each numbered directory N, there are three files: (1) data.N contains the simulated MSA in PHYLIP format; (2) model.N contains the best-fit model detected from the corresponding original MSA; (3) tree.N contains the tree (in Newick format) inferred from the corresponding original MSA. tree.N and model.N are used by Seq-Gen to simulate the MSA in data.N.</li> <li>The "aa" subdirectory is organized similarly for 6,165 AA MSAs.</li> </ul> <p>After being uncompressed, the TreeBASE dataset comprises 115 files corresponding to 115 MSAs. There are:</p> <ul> <li>70 DNA MSAs in PHYLIP format. These files follow the naming scheme dna_[number of sequences]_[number of sites].phy.</li> <li>45 protein MSAs in PHYLIP format. These files follow the naming scheme prot_[number of sequences]_[number of sites].phy.<br> </li> </ul>
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers> 50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. The letter A corresponds to a clade referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–3 and 5–6.
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 3. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with concatenated ITS2 and 28S DNA sequences from 41 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers> 50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. Letters A and B correspond to clades referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–2 and 4–6.
Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approaches
Open the record for dataset details and reuse information.
FIGURE 36. Maximum parsimony tree for cytochrome b in Two new species of oak gall wasps from Turkey (Hymenoptera: Cynipidae Cynipini)
FIGURE 36. Maximum parsimony tree for cytochrome b sequences indicating the relationships of Cynips izzetbaysali sp. nov. and Callirhytis afion, sp. nov. to other Cynipini species. GenBank Accession number for each species used in the analysis is given with the species names. Two new species included in the analysis are coloured in red. Numbers above nodes indicate posterior probability support values.
FIGURE 4. Maximum parsimony cladogram depicting phylogenetic relationships among 11 isolates representing 4 in First record of Hexaglandula corynosoma (Travassos, 1915) Petrochenko, 1958 (Acanthocephala: Polymorphidae) in intermediate and definitive hosts in Mexico
FIGURE 4. Maximum parsimony cladogram depicting phylogenetic relationships among 11 isolates representing 4 species of polymorphids. Numbers in internodes represent bootstrap support values for the Neighbor-Joining and Parsimony analyses, respectively. * = Cystacanth of Hexaglandula corynosoma.
FIGURE 58. Maximum parsimony strict consensus tree. Bootstrap proportions from 1000 in Taxonomic revision and phylogeny of the ant genus Prenolepis (Hymenoptera: Formicidae)
FIGURE 58. Maximum parsimony strict consensus tree. Bootstrap proportions from 1000 replicates are presented along the branches.
FIGURE 3. Maximum parsimony phylogenetic relationships with the taxon Pituna poranga removed. Heuristic search with 50 in Description of a new annual rivulid killifish genus from Venezuela
FIGURE 3. Maximum parsimony phylogenetic relationships with the taxon Pituna poranga removed. Heuristic search with 50 random additions and TBR branch swapping resulted in a single most parsimonious topology of 5706 steps. Numbers above nodes are bootstrap values based on 2000 pseudoreplicates (25 random additions each); only values over 50 are reported. Numbers below branches are Bremer support indices which are equivalent to unreversed synapomorphies.
FIGURE 2. Maximum parsimony phylogenetic hypothesis. Heuristic search with 50 in Description of a new annual rivulid killifish genus from Venezuela
FIGURE 2. Maximum parsimony phylogenetic hypothesis. Heuristic search with 50 random additions and TBR branch swapping resulted in a single most parsimonious topology of 6206 steps. Numbers above nodes are bootstrap values based on 2000 pseudoreplicates (25 random additions each); only values over 50 are reported. Numbers below branches are Bremer support indices which are equivalent to unreversed synapomorphies.
FIGURE 5. Maximum Parsimony majority rule consensus tree from 33 in Revision of the genus Caenota Mosely (Trichoptera: Calocidae), with descriptions of 2 new species and the larva of C. nemorosa Neboiss
FIGURE 5. Maximum Parsimony majority rule consensus tree from 33 morphological characters of 7 species of Caenota and 1 species of Tamasia. Values on the branches are bootstrap values calculated from 1000 bootstrap replications.
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a in A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a number of named, primarily Palaearctic taxa included. Species groups that are characterizable morphologically and discussed are indicated in different colours. The tree is rooted using Heterogamus species.
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches.
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
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