NINJA Crack + Full Version
Algorithm: Neighbor-Joining, distance-based method;
Inputs: PHYML input files (joint trees and the distance matrices), percent divergence threshold, species outgroup, random number seed
Parsing tree input: parses tree file to create one neighbor for each taxon, and one e-value for all of them
Parses the distance matrix to generate the distance values of each pair in the matrix, and outputs the final distance matrix
Parses the distance matrix: NINJA sets the ranges of the first/second half of the matrix (if there are more than two) to cover all possible distances (e.g. from -1 to 1)
Parses the alignment to generate the appropriate number of input-to-output and output-to-input edges for the pairs
Calculates the squared distance of each pair
Calculates the matrix product of the pair distance values and scales the product to the values' maximum distance
Calculates the e-value as the scaled distance matrix multiplied by 10^(-distance)
Calculates the input-to-output and output-to-input distances
Converts the output-to-input distances to the pairwise distance matrix by adding the input-to-output distance and the output-to-input distance
Converts the output-to-input distances to the distance matrix by subtracting the input-to-output distance and the output-to-input distance
Converts the input-to-output distances to the distance matrix by adding the input-to-output distance and the output-to-input distance
Converts the input-to-output distances to the distance matrix by subtracting the input-to-output distance and the output-to-input distance
Converts the scaled distance matrix to a distance percentage matrix
Converts the scaled distance matrix to a distance matrix
Parses user-selected distance functions
Scales all e-values to the maximum
Plots tree
Saves the tree
Performs the distance calculation and writes the trees to files, distance matrices, and distance percentage matrices
Plots the pairwise distance percentage matrix and the distance matrix
Plots the tree
Performs the distance calculation and writes the trees to files, distance matrices, and distance percentage matrices
Plot the tree
NINJA Crack
NINJA Cracked 2022 Latest Version is the nighbour joininG toolkit. It ia fast, easy-to-use, command line-based and platform independent. NINJA can be used for phylogeny inference. It can be used by biologists, taxonomists and statisticians. NINJA can also be used in a range of applications.
Using NINJA:
NINJA is a command line java based program. This file is quite large (~ 1.5MB). So, It needs quite some memory to start. This program was written to be as platform independent as possible. It can be used on Windows, Mac OS X and Linux.
It was not  written with any specific requirements in mind. 
Installation:
Make sure you have installed Java (default installation may be enough).
You will need to do some configuration to make NINJA work.
You can find the instructions here:
NINJA Installation Instructions
Input Format:
The input to NINJA can be multiple alignment and distance matrices.
The alignment can be supplied as plain text file or in multiple sequence format 
(eg: tab-delimited, maf).
The sequence data needs to be encoded in an ASCII format. NINJA supports the following options for multiple sequence format:
ClustalW
Multiple sequence alignment with at the beginning of each line a '>' 
'>'
MSF 1
Protocols for Minimum-SST File for protein sequences
MSF 2
The basic format of a protein sequence as defined by Smith and Waterman 
It is structured as follows:
Column 1:
Intact protein sequence
Columns 2,...:
Removal of the N-terminal Met in Column 2
Removal of the C-terminal Tyr in Column 3
Note: It is possible to specify amino acid types with a one letter code and only one or two columns per residue. 
The first or the last 15 residues of the protein sequence are not included in the alignment.
ntpair/ww
It converts your output into the standard W matrix format. The alignment 
includes 16 random sequences.
Sequence format (excluding alphabetical characters):
Alphabetical characters:
15    
T    
I
f0d5c1b395

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