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      Revision of the genus Euagathis Szépligeti (Hymenoptera, Braconidae, Agathidinae) from Thailand, with description of three new species

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      Journal of Hymenoptera Research

      Pensoft Publishers

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          Abstract

          The species of the genus Euagathis Szépligeti (Hymenoptera, Braconidae, Agathidinae) from Thailand are revised. Eight species are treated, three new species are described, i.e. Euagathis breviantennata sp.n., E. setosimaculata sp. n. and E. pallitarsis sp. n. Disophrys sogdiana Fahringer, 1937, D. chinensis Fahringer, 1937, and Euagathis sentosus Chen & Yang, 1995, are new junior synonyms of Euagathis chinensis (Holm‑gren, 1868). Euagathis guangxiensis (Chen & Yang, 2006) is a new combination. Lectotypes are designated for Disophrys sogdiana Fahringer, 1937, and D. chinensis Fahringer, 1937. A dichotomous illustrated key to species is presented; links to electronic interactive keys and to distribution maps are also included.

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          The general stochastic model of nucleotide substitution.

          DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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            GUIDANCE: a web server for assessing alignment confidence scores

            Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE web-server, a user-friendly, open access tool for the identification of unreliable alignment regions. The web-server accepts as input a set of unaligned sequences. The server aligns the sequences and provides a simple graphic visualization of the confidence score of each column, residue and sequence of an alignment, using a color-coding scheme. The method is generic and the user is allowed to choose the alignment algorithm (ClustalW, MAFFT and PRANK are supported) as well as any type of molecular sequences (nucleotide, protein or codon sequences). The server implements two different algorithms for evaluating confidence scores: (i) the heads-or-tails (HoT) method, which measures alignment uncertainty due to co-optimal solutions; (ii) the GUIDANCE method, which measures the robustness of the alignment to guide-tree uncertainty. The server projects the confidence scores onto the MSA and points to columns and sequences that are unreliably aligned. These can be automatically removed in preparation for downstream analyses. GUIDANCE is freely available for use at http://guidance.tau.ac.il.
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              Revision of the Agathidinae (Hymenoptera: Braconidae) with comparisons of static and dynamic alignments

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                Author and article information

                Journal
                Journal of Hymenoptera Research
                JHR
                Pensoft Publishers
                1314-2607
                1070-9428
                February 14 2014
                February 14 2014
                : 36
                : 1-25
                Article
                10.3897/jhr.36.5658
                © 2014
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