Conserve IV is an application for calculating diversity in site-based conservation and assessing preservation schemes. Specifically, it calculates diversity metrics over a phylogeny or series of phylogenies. Individual taxa can be included or excluded from calculations, simulating the state of their preservation and possible accompanying loss of evolutionary history. Taxa can be grouped into sets manually or via several automatic methods, and these sets activated or inactivated as one. Where multiple phylogenies are provided, confidence limits are calculated for diversity metrics. Finally, capability is provided for summing external costs, expenditure that is specific to preserving individual taxa.
Paul-Michael Agapow and Austin Burt (email@example.com), Dept. Biology, University College London
CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.
CPC (Coding Potential Calculator) is a software to assess the protein-coding potential of a transcript (i.e whether a cDNA/RNA transcript could encode a peptide or not) based on six biologically meaningful sequence features. Tenfold cross-validation on the training dataset and further testing on several large datasets showed that CPC can discriminate coding from noncoding transcripts with high accuracy. Furthermore, CPC also runs an order-of-magnitude faster than a previous state-of-the-art tool and has higher accuracy.
APOLLO pairwise is a program to assess the quality of a pool of structure models predicted for a protein. Teh software evaluates the absolute and/or relative qualities of multiple models or a single model
ANOLEA (Atomic Non-Local Environment Assessment) is a server to assess the quality of a three – dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.
TOROCOR is designed (1) to characterise the spatial autocorrelation of quantitative and/or qualitative variables and (2) to test the significance of the association between variables, notably using torus-translation randomisations. The latter procedure removes the bias of classical tests applied on spatially autocorrelated variables where samples cannot be considered as independent (classical tests tend to be liberal, i.e. rejecting too often the null hypothesis that there is no association between variables).
Epistasis-HS allow you to assess the degree of epistasis for a given trait between a pair of maternal or paternal half-sib families. You are only able to use this program to calculate epistasis between a pair of half-sib families. If your mating structure involves multiple half-sib families (i.e., k > 2) you will need to recalculate estimates among all the possible pairwise half-sib groupings (i.e., k*(k-1) / 2 pairwise combinations).