Simulation results: Ne = 1.0E4

Results of evolutionary simulations for Ne = 1.0E

Simulation results: Ne = 1.0E6

Results of evolutionary simulations for Ne = 1.0E

Simulation results (null amino acid): Ne = 1.0E4

Results of evolutionary simulations for Ne = 1.0E4: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering

Simulation results: Ne = 1.0E8

Results of evolutionary simulations for Ne = 1.0E

Ancestral relationships among LAVA elements.

<p>The predicted network of LAVA ancestral relationships is shown. A) All sequences that replicated with probability >30% are represented as nodes in the network. Arrows are drawn between sequences if there was at least 5% probability that an ancestral relationship existed between those sequences, with the direction of the ancestor-descendant relationships indicated by the arrows. Sequences are colored based on their CoSeg subfamily assignments (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004482#pgen.1004482.s005" target="_blank">Table S2</a>). Sequences colored white do not exist in the data, but are inferred to have existed ancestrally. B) The network in A is modified by the addition of all extant TEs in the data added to the network as nodes represented by small dots. Edges are drawn between an element and an ancestral sequence if there was at least 5% probability the element descended from the ancestral sequence. Nodes are colored based on CoSeg subfamily assignment.</p

Number of replicative sequences identified for different prior penalties in LAVA and <i>Alu</i>Sc.

<p>Number of replicative sequences identified for different prior penalties in LAVA and <i>Alu</i>Sc.</p

Inference of Transposable Element Ancestry

<div><p>Most common methods for inferring transposable element (TE) evolutionary relationships are based on dividing TEs into subfamilies using shared diagnostic nucleotides. Although originally justified based on the “master gene” model of TE evolution, computational and experimental work indicates that many of the subfamilies generated by these methods contain multiple source elements. This implies that subfamily-based methods give an incomplete picture of TE relationships. Studies on selection, functional exaptation, and predictions of horizontal transfer may all be affected. Here, we develop a Bayesian method for inferring TE ancestry that gives the probability that each sequence was replicative, its frequency of replication, and the probability that each extant TE sequence came from each possible ancestral sequence. Applying our method to 986 members of the newly-discovered LAVA family of TEs, we show that there were far more source elements in the history of LAVA expansion than subfamilies identified using the CoSeg subfamily-classification program. We also identify multiple replicative elements in the <i>Alu</i>Sc subfamily in humans. Our results strongly indicate that a reassessment of subfamily structures is necessary to obtain accurate estimates of mutation processes, phylogenetic relationships and historical times of activity.</p></div

var_sharing_sampling

calculates pairwise similarity of genotypes between samples of a vc

cutgenome.v0.04

Returns .bed file with double digested fragments from a provided genome and cut site

check_radtag_from_sam

counts the number of times a provided restriction site sequence is found at the beginning of a sequence read from a .sam fil