Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.

/pdf/modeltest-testing-the-model-of-dna-substitution-2dmippvvyz.pdf

MODELTEST: testing the model of DNA substitution.

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

https://www.zora.uzh.ch/id/eprint/155669/1/ZORA_NL_155669.pdf

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.

16S ribosomal DNA amplification for phylogenetic study.

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.

/pdf/jmodeltest-phylogenetic-model-averaging-4hpp3p5d0f.pdf

jModelTest: Phylogenetic Model Averaging

Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282--283, Bioinformatics, 18, 77--82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.

Availability: http://cd-hit.org

Contact: [email protected]

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Polysome profiles obtained from mammalian tissues by an improved procedure

Loss of ribonucleic acid into lipid solvents after acid precipitation.

The nature and relative quantity of insulin-like growth factor (IGF) receptors in rat placental microsomal membranes was investigated by competitive binding studies and covalent cross-linking followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Binding studies revealed that 100 fig membrane protein specifically bound 26.5% of [125I]iodo-IGF-II, 19.6% of [125I]iodomultiplication-stimulating activity III-2 ([125I]iodo-MSA-III-2), and 11.5% [125I]iodo-IGF-I. IGF-II was equipotent with MSA-III-2, and both were approximately twice as potent as IGF-I in competing with [125I]iodo-IGF-I for binding. In contrast, IGF-I competed for the binding of [1Z5I]iodo- MSA and [125I]iodo-IGF-II with only 5–20% the potency of unlabeled MSA and IGF-II. Insulin competed weakly with [126I] iodo-IGF-I for binding (achieving half-maximal displacement at 20 μg/ml), but did not compete with [125I]iodo-MSA for binding. This evidence suggested that while IGF-I binds to both IGF-I and IGF-II receptors, the majority of...

Insulin-Like Growth Factor Receptors in Rat Placental Membranes

Creatine kinase activity is associated with different isozyme species. We have examined two of these: the cytoplasmic brain (B) isozyme that is expressed in many tissues and is reported to be induced by estrogen and the developmentally regulated cytoplasmic muscle (M) isozyme that is found predominantly in differentiated muscle tissue. Recently, we cloned and sequenced the cDNA for the M isoenzyme of rabbit creatine kinase. We now report the isolation of B-isozyme cDNAs and the deduced primary structure of the polypeptide. The translated cDNA nucleotide sequence was cross-checked by fast-atom bombardment/mass spectrometry of tryptic fragments from the protein. The sequence is exactly colinear with the rabbit M isozyme and the two isozymes have 80% nucleotide and amino acid sequence identity. There are blocks of 36 and 41 amino acids where the amino acid sequence is conserved exactly. The colinearity of the two sequences and the extent of their identity makes it unlikely that either isozyme has unique polypeptide domains that account for specialized functions. The rationale for the existence of these creatine kinase isozymes, with distinct biological features, evidently is at the level of regulation of individual isozyme expression.

https://www.pnas.org/content/pnas/82/8/2310.full.pdf

Hamish N. Munro

Papers

Polysome profiles obtained from mammalian tissues by an improved procedure

Loss of ribonucleic acid into lipid solvents after acid precipitation.

Insulin-Like Growth Factor Receptors in Rat Placental Membranes

Two tissue-specific isozymes of creatine kinase have closely matched amino acid sequences

The influence of dietary protein on the incorporation of 14C-glycine and 32P into the ribonucleic acid of rat liver.