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Genome annotation. (XLSX 9 kb

meristics

Counts of meristic characters in Tilapia zillii. TAUP numbers are voucher specimens deposited in the National Collection of Natural History at Tel- Aviv University. Populations of origin are denoted as follows: TM, Taninim (coastal); EA, Ein Afek (coastal); KN, Kishon (Kishon); KT, Kinneret (Jordan); BS, Beit She’an (Jordan); EF, Ein Feshkha (Dead Sea); NH, Ne’ot HaKikar (Dead-Sea introduced); RG, Ramat Gan (coastal introduced); NM, Nitzanim (coastal introduced); MA, HaMa'apil (coastal introduced). The characters considered are denoted as follows: LL1, Number of scales along the upper lateral line; LL2, Number of scales along the lower lateral line; TR1, Number of scales between the dorsal fin and the upper lateral line; TR2, Number of scales between the upper and lower lateral line; TR3, Number of scales between the lower lateral line and the anal fin; P, Number of rays in the pectoral fin; Pbr, Number of branched rays in the pectoral fin; V, Number of rays in the ventral fin; Vbr, Number of branched rays in the ventral fin; D, Number of rays in the dorsal fin; Dbr, Number of branched rays in the dorsal fin; DS, Number of spikes in the dorsal fin; A, Number of rays in the anal fin; Abr, Number of branched rays in the anal fin; AS, Number of spikes in the anal fin; C, Number of rays in the caudal fin; Cbr, Number of branched rays in the caudal fin; LPR, The position of the longest pectoral ray; LVR, The position of the longest ventral ray; LDR, The position of the longest dorsal ray; LAR, The position of the longest anal ray; GR, The number of gill raker

Summary of the Python module structure.

<p>Summary of the Python module structure.</p

The phylogenetic workflow as a single Python object.

<p>(A) The workflow is contained as a single object with bins (attributes) for the raw data and metadata, as well as for the various workflow analyses and forks. These are made provenance-explicit with unique IDs and names. (B) Analyses are invoked via commands that modify the workflow object. A command can invoke batch analysis for all the relevant data in the object. For example, the command ‘align’ will apply for all the unaligned datasets. Commands can be limited to certain datasets using IDs. Commands can be customized using options. (C) Provenance survives version changes. The workflow object can be serialized (pickled) and then committed to a version control repository as a single file. Reverting to previous output version will also revert to the intermediate steps leading to it. Forks can be done post-hoc using the all-inclusive and provenance explicit workflow (pickled) object.</p

El defensor : Diario Liberal independiente, protector de los intereses materiales y morales de esta provincia: Año III Epoca segunda Número 300 - 1905 febrero 11

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

A typical ReproPhylo workflow.

<p>This illustration demonstrates the flow of data (blue arrows) and metadata (red arrows) through the phylogenetic analysis. Numbers on arrows correspond with code snippets in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004447#pcbi.1004447.s002" target="_blank">S1 Methods</a>. Asterisks indicate an automatic pickle and Git checkpoint. The user can toggle between these checkpoints indefinitely using a built in ReproPhylo function.</p

Schematic description of the workflow utilized in this study.

<p>A flow chart of the analysis steps described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106630#s2" target="_blank">Material and Methods</a> section, including the homology searches for YRE protein domains, the classification of YREs based on their features, the phylogenetic reconstruction of YRE relationships and their phylogenetic classification.</p

The diversity of tyrosine recombinase elements (YREs) and their diagnostic features for taxonomic classification.

<p>The known taxonomic distribution of each element (A–H) is listed along with a cartoon of its structure. Metazoa are in bold font and Ecdysozoa are underlined. The features considered are the presence and absence of the reverse transcriptase (RT), methyltransferase (MT) and tyrosine recombinase (YR) domains and their orientation (grey triangles), as well as the presence, absence and position of split direct repeats (pairs of triangles, sharing a colour and pointing in the same orientation), inverted repeats (pairs of triangles, sharing a colour and pointing in opposite orientation) and zinc finger motifs from the Gag protein. Where a question mark is indicated, some members of the group possess and others lack a zinc finger motif.</p

The distribution of YREs among Nematoda and outgroup species.

<p>The phylogenetic tree of Nematoda is based on De Ley and Blaxter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106630#pone.0106630-DeLey1" target="_blank">[47]</a> and Kiontke et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106630#pone.0106630-Kiontke1" target="_blank">[48]</a>. Element types are colour coded. The phylogenetically classified YRE matches in each species are indicated. Pie-charts represent the proportion of each element type with their radii proportional to the number of phylogenetically classified YRE matches.</p

Mean contig lengths, contig length at N50 and PSIBLASTN putative transposable element counts of the genomes analysed.

<p>YR matches are shown, of which, the number of YREs that were classified based on their features (intact YREs) and their phylogenetic position (Partial YREs) is indicated. In addition, the counts of RT hits from BEL, <i>Copia</i> and <i>Gypsy</i> LTR elements are indicated for each species. Matches were found in all the species in at least one of the PSITBLASTN searches. The number of matches found in each species seems to be detached from the mean contig length or contig length at N50 in the species' genome assembly.</p><p>Mean contig lengths, contig length at N50 and PSIBLASTN putative transposable element counts of the genomes analysed.</p