Software Listing: Amino Acid Alignment

PutGaps is a simple command line utility designed to insert gaps into DNA alignment files by using the amino acid equivalent. The program can be used for conserving codon positions into aligned nucleotide and amino acid files.

You can use the program in the console in order to view the available commands and enter the operation arguments.


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  • Platform: WinOther
  • MAFFT
  • License: Shareware
  • Rating

MAFFT was developed as a small, easy-to-use and Command Line-based multiple sequence alignment application.

MAFFT is a software that offers a range of alignment methods for amino acid or nucleotide sequences.


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  • Platform: Win7 x64, Windows 7, Windows 8, WinOther, WinVista

Multifunctional Biochemistry Software Package Integrated With: Amino Acid Analysis, Building Block Composition, Digestion, Elemental Analysis, Fragmentation, Isotopic Distribution, Combinatorial Library, Molecular Weight, Motif, and Helix Wheel/Net..

  • Platform: Win2000, Win7 x32, Win7 x64, WinOther, WinVista, WinVista x64

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. It is free software under GPLv2+. Requested Features: - Import of Vector NTI Database/Data - Export of Map as Vector Graphic - Edit and move around Plasmid Map Layout - Allow storage in database of complete sequencing files (if space is a concern maybe an upper limit of 2 sequences for each clone would suffice) - Add sections in the database to allow record of box storage position of clone's DNA, glycerol stock, primers - Allow closing of files with Ctrl-W - Clicking a region in the vector map should take the cursor to that region in the sequence viewer.

  • Platform: WinOther

Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them.

  • Platform: Linux, Mac OS X, WinOther

Pseudo amino acid composition or PseAAC, is designed as an accessible and Open Source algorithm that could convert a protein sequence into a digital vector that could be processed by pattern recognition algorithms.

The design of PseAAC Builder incorporated the sequence order information to improve the conventional amino acid compositions.

The application of pseudo amino acid composition is very common, including almost every branch of computational proteomics.

You can now use the cross-platform PseAAC-Builder tool for generating protein pseudo-amino acid compositions.

  • Platform: WinOther

The Protein Stability program was developed to help you explore and analyze the energy requirements of each amino acid in the protein sequence derived from various applied kinetic and thermodynamic quantities.

The algorithm is strongly dependent both on kinetic quantities such as atomic solvation energies and solvent accessible surface area and thermodynamic quantities viz. enthalpy, entropy, heat capacity, etc.

The hydrophobicity pattern of protein was considered as the important component of protein stabilization.

Protein stability, the most important aspect of molecular dynamics and simulations, requires sophisticated instrumentations of molecular biology to analyze its kinetic and thermodynamic background.

  • Platform: WinOther

Having trouble remembering the one letter, three letter amino acid names? How about the polarity? Use this App as a quick reference to learn..

  • Platform: Android 4.x
  • McRate
  • License: Freeware
  • Price: 0.00
  • Rating

McRate is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA). In contrast to other existing programs McRate considers all possible phylogenetic scenarios among the sequences under study, rather than relying on a single best tree..

  • Platform: WinOther

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between these distance values. In pairwise distance methods, the dissimilarity (fraction of substitutions) is usually converted into evolutionary distance by correcting for multiple mutations. The most frequently used equations to convert dissimilarities into distances are implemented in TREECON.

  • Platform: WinOther
  • Simprot
  • License: Freeware
  • Price: 0.00
  • Rating

Simprot allows for several models of amino acid substitution (PAM, JTT
and PMB), allows for gamma distributed sites rates according to Yang's model, and implements a
parameterised Qian and Goldstein distribution model for insertion and deletion..

  • Platform: WinOther

ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically..

  • Platform: WinOther

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution..

  • Platform: Linux, Mac OS X, WinOther
  • ATGC
  • License: Freeware
  • Price: 0.00
  • Rating

ATGC is an application containing a pack of useful algorithms in user-friendly interface for aligning nucleotide sequences, searching consensus and restriction sites, predicting amino acid sequence, docking contigs and so on..

  • Platform: WinOther
  • BASILISK
  • License: Freeware
  • Price: 0.00
  • Rating

BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein's backbone..

  • Platform: Linux, Mac OS X
  • BiasViz
  • License: Freeware
  • Price: 0.00
  • Rating

BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments..

  • Platform: Linux, Mac OS X, WinOther

This application transcribes basic codons and tells you the amino acid it codes for, the tRNA anti-Codon, and give you a 3D structural model of the amino acid and 2D picture of its chemical structure. Analysis reports can then be printed by the user..

  • Platform: WinOther
  • CodonW
  • License: Freeware
  • Price: 0.00
  • Rating

CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information..

  • Platform: Linux, Mac OS X, Unix, WinOther
  • iso2l
  • License: Freeware
  • Price: 0.00
  • Rating

iso2l (E?aisEâ„¢utuE?l, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain..

  • Platform: Linux, Mac OS X, WinOther

MatrixGen is a Bioinformatics application used to generate scoring matrices from analysis of aligned Amino Acid and DNA data sets. These matrices can then be used by Clustal to generate more accurate alignments. Based upon the Henikoff BLOSUM method..

  • Platform: Linux, Mac OS X, Unix, WinOther

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