In the final step of reconstruction, we use the CONSENSE program, which is a part of the PHYLIP software package, to compute an unrooted consensus tree [ 25].
As the first step of reconstruction of the evolutionary processes in this species, we investigated its phylogenetic position based on 11 whole mitochondrial genome sequences including the newly determined ones of the whale-fall lancelet A. inferum and two coral-reef congeners.
The reconstruction process requires intensive manual curation effort, though recent progress has made it possible to automate some steps of the reconstruction process.
In this work, we analyzed the framework of ICON and classified the operations of major steps of ICON reconstruction into three types.
Entering through Jaffa Gate, I go into the Tower of David Museum and climb the steps of a reconstruction of Phasael's Tower, another project of Herod's, which he named for his brother.
For each of these steps, a job can be defined, which means that intermediate output can be generated, in order to let users exploit external tools or collaborations for maximum customization of all the steps of the reconstruction workflow.
The classical steps of ovarian reconstruction are achieved without complex instrumental manipulation by complete adhesiolysis and mobilization of the ovary, followed by opening of the pseudocavity at the site of invagination and rinsing of the chocolate content and finally bipolar ablation of the superficial endometriotic tissue.
The next steps of regulon reconstruction were done with RegPredict, a web-tool for comparative genomic analysis (21).
In the following, we discuss the the main steps of the reconstruction algorithm in more detail and provide information for an efficient implementation.
All compute intensive steps of the reconstruction algorithm have a high degree of locality: A major part of the operations, e.g. the assembly of the system matrices or the sensitivity, can be performed in an element-by-element fashion.
