SENDBS Crack 2022 [New]
SENDBS 2022 Crack computes average nucleotide substitutions within and between populations under the standard neutral theory of molecular evolution and assigns a test statistic to each pair of species. Average nucleotide substitutions between populations are approximated by the frequency-weighted average of nucleotide differences at single loci. The multilocus context is taken into account by modeling the site-specific variation of transition/transversion ratios as a function of the number of pairs of homologous sites. SENDBS is highly parameter-sensitive and calculates correctly the parameter values that optimally fit the observed data. It also computes the standard error of average nucleotide substitutions.
SENDBS computes the standard error of the average nucleotide substitutions in a similar way as Nei and Jin (1987) did, using a bootstrap method. SENDBS does not rely on the assumption that the loci are selectively neutral, since the evolution of all loci is modeled simultaneously.
SENDBS computes standard errors of average nucleotide substitutions with a bootstrap method by resampling sites, which is different from Nei and Jin’s method. Also, sensbs constructs a population tree with a neighbor-joining method.
SENSBS computes average nucleotide substitution rates between species and reconstructs a neighbor-joining tree.
SENSBS is a successor of the program Kishino-Hasegawa (KH) that was developed and is maintained by Koike et al. (1997). It is based on a coalescent model that takes account of the multilocus context. It computes average nucleotide substitution rates between species and reconstructs a neighbor-joining tree. It is thus a suitable alternative to the software RAxML (Stamatakis 2006) if you are interested in calculating average nucleotide substitution rates.
Note that SENSBS does not fit the assumptions made by KH, which might cause the reconstructed tree to differ. Also, sensbs requires a data file that contains, for each pair of species, the coding sequences that compose the sequences used to calculate average nucleotide substitution rates.
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SENDBS computes average nucleotide substitutions within and between populations.
SENDBS is useful for species-level studies, such as the phylogenetic analysis of HIV subtypes, identification of migration events between genetically distinct populations or detection of diversifying selection.
SENDBS uses a method of computing standard errors of average nucleotide substitutions developed by Nei and Jin (1987) and implemented in the program SITES.
When multiple sequences of the same species are compared, SENDBS computes an average per-site sequence divergence, taking into account the length and frequency of different bases at each site.
However, SENDBS uses a bootstrap method to compute standard errors of average nucleotide substitutions.
SENDBS performs statistical tests to detect whether or not the difference between two populations is statistically significant.
If the test statistic is small (e.g. 1.0), then the difference is significantly different from zero; otherwise, it is not significantly different from zero.
SENDBS can either (1) construct a neighbor-joining population tree or (2) compute average nucleotide substitutions between populations by resampling the sites.
If we choose resampling, SENDBS uses the following two sampling methods, referred to as the “per-site resampling method” and the “bootstrap resampling method”, respectively.
In the per-site resampling method, sites are resampled with replacement so that the total number of sites is equal to the original number of sites.
On the other hand, in the bootstrap resampling method, sites are resampled without replacement so that the number of sites per population is equal to the original number of sites.
In addition, SENDBS can be used in both unrooted and rooted tree formats.
SENDBS does not assume that the data is unrooted or rooted.
When the data is rooted, the population tree will be displayed as a rooted tree.
When the data is unrooted, it will be displayed as an unrooted tree.
In the per-site resampling method, the number of resampled sites is determined by the following parameters:
maxsites – maximum number of sites to be used for resampling
nc – number of populations to be compared
The results of resampling for the per-site resampling method are based on the program SITES version 2.01, which is found at
What’s New in the SENDBS?
SENDBS computes average nucleotide substitutions within and between populations under the Kimura two-parameter (K2P) model. K2P uses a constant nonsynonymous substitution rate and a variable transition/transversion rate. When estimating divergence time, SENDBS assumes that the change in the synonymous substitution rate is negligible and that there are no change in population size. SENDBS provides average number of nucleotide substitutions per site (using K2P), average number of nucleotide substitutions per synonymous site (using K2P), average number of nucleotide substitutions per nonsynonymous site (using K2P), average number of nucleotide substitutions per synonymous site under the K2P model and maximum likelihood (ML) estimates of the substitution rate (using the K2P model) with their standard errors. SENDBS also provides a file of the average number of nucleotide substitutions per site and maximum likelihood estimates of the substitution rate as a population tree. The population tree was computed using the neighbor-joining method implemented in PAUP\*.
SENDBS has 3 categories of data inputs:
Tree file (stored as the SENDBS data file): a list of characters, a list of vectors and two integer vectors for tree length and population sizes, respectively.
Mutation rate file (stored as the SENDBS data file): a list of characters with the names of the branch lengths, which is necessary for the estimation of substitution rate (K2P model).
Population file (stored as a SENDBS data file): a list of characters, a list of vectors and an integer vector for population size, respectively.
SENDBS provides the following outputs:
Output File: a SENDBS data file containing the above-mentioned information.
Average number of nucleotide substitutions per site (using K2P model): the average number of nucleotide substitutions per site (assuming the K2P model) between two populations.
Average number of nucleotide substitutions per synonymous site (using K2P model): the average number of nucleotide substitutions per synonymous site between two populations.
Average number of nucleotide substitutions per nonsynonymous site (using K2P model): the average number of nucleotide substitutions per nonsynonymous site between two populations.
Average number of nucleotide substitutions per synonymous site (using K2P model) and maximum likelihood estimates of the substitution rate (using the K2P model): the average number of nucleotide substitutions per synonymous site and maximum likelihood estimates of the substitution rate (using the K2P model) between two populations.
Pairwise Substitution Calculations:
SENDBS computes the number of nucleotide substitutions from each population pair and computes the average of these numbers. Therefore, SENDBS does not distinguish between changes in the nonsyn
System Requirements For SENDBS:
Windows 7, Windows 8, Windows 8.1
1 GHz PC
1024 MB RAM
2 GB free hard disk space
DirectX 9 or later
ATI Radeon HD 2600 XT, HD 4000, HD 5000, or HD 6000 series
NVIDIA GeForce 8400 GS, GTX 800, GTX 810, GTX 850, GTX 900, GTX 1000 series
1400 MB disk space is recommended