Genome Sequence of the Pea Aphid Acyrthosiphon pisum
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Cites methods from "Genome Sequence of the Pea Aphid Ac..."
...2010), ETE has been widely used as a computational framework to perform numerous phylogenomic analyses, including characterizing newly sequenced genomes (Richards et al. 2010; Wang et al. 2014), extracting information from large sets of phylogenetic trees (Derelle and Lang 2012; Chiapello et al....
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...…ETE has been widely used as a computational framework to perform numerous phylogenomic analyses, including characterizing newly sequenced genomes (Richards et al. 2010; Wang et al. 2014), extracting information from large sets of phylogenetic trees (Derelle and Lang 2012; Chiapello et al. 2015;…...
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References
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"Genome Sequence of the Pea Aphid Ac..." refers methods in this paper
...We then built one consensus per group with the MAFFT [118] multiple sequence alignment program and classified each consensus (1) according to BLASTER matches using TBLASTX and BLASTX [114] with the entire Repbase Update databank [119] and (2) according to the presence of structural features such as terminal repeats (TIR, LTR, and polyA or SSR tails)....
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...In the first part of the pipeline, consensus TEs were predicted ab initio by first searching for repeats with BLASTER for an all-by-all BLASTN [114] genome comparison and then results grouped using three clustering methods—GROUPER [115], RECON [116], and PILER [117]—with default parameters....
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16,261 citations
"Genome Sequence of the Pea Aphid Ac..." refers methods in this paper
...4 [105], using JTT as an evolutionary model and assuming a discrete gammadistribution model with four rate categories and invariant sites, where the gamma shape parameter and the fraction of invariant sites were estimated from the data....
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...4 [105], using JTT as an evolutionary model and assuming a discrete gamma-distribution model with four rate categories and invariant sites, where the gamma shape parameter and the fraction of invariant sites were estimated from the data....
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12,003 citations
"Genome Sequence of the Pea Aphid Ac..." refers methods in this paper
...We then built one consensus per group with the MAFFT [118] multiple sequence alignment program and classified each consensus (1) according to BLASTER matches using TBLASTX and BLASTX [114] with the entire Repbase Update databank [119] and (2) according to the presence of structural features such as terminal repeats (TIR, LTR, and polyA or SSR tails)....
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10,262 citations
"Genome Sequence of the Pea Aphid Ac..." refers methods in this paper
...For each protein encoded in the pea aphid genome, a SmithWaterman [106] search (e-val 1023) was performed against the above mentioned proteomes....
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...For each protein encoded in the pea aphid genome, a SmithWaterman [106] search (e-val 10(23)) was performed against the above mentioned proteomes....
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8,757 citations