WGBS: The sequence reads were aligned to either strand of the HG19 reference genome using a custom computational pipeline.
An. albimanus transcripts were aligned to either genome using Exonerate v. 2.2 [ 79] with the EST2 Genome mode, and a threshold score of 300, and maximum intron length of 20,000 bp.
An alignment is characterized by the number of matches m, that of mismatches f, that of gaps g i in s i and that of gaps g j in s j.The length of s i is equal to m + f + g j and that of s j is m + f + g i, because any letter in s i is aligned to either a letter in s j or gap symbol in s j and vice versa.
Inner nodes can either be aligned to a leaf node or to another inner node (profile-profile alignment).
An analyzer was placed in the imaging path and consisted of a linear polarizer (25mm PL, Tamron, Japan) which was aligned to detect either the scattered light polarization parallel or perpendicular to the incident laser light.
Switchgrass BACs were aligned to each other using either blastz at the Pipmaker [ 45] server (http://pipmaker.bx.psu.edu/pipmaker/) or mVISTA [ 46] server (http://genome.lbl.gov/vista/) using the LAGAN [ 47] algorithm.
The consensus sequences for each gene in both sexes of either strain were aligned to each other and to the Celera strain [ 35] from FlyBase Release 3.0, used as a reference, with ClustalW on Biology Workbench 3.2 [ 36] with default alignment parameters.
A total of 10 922 spots were aligned to the same unigene using either the 3′ or the 5′ end sequences.
Reads that passed quality checks were aligned to the F. vesca genome using either a custom script or SeqMan NGen (DNASTAR version 2.3, Lasergene, Madison, WI, USA).
