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 | [ABySS](http://www.bcgsc.ca/platform/bioinfo/software/abyss) | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
 | [almost](http://www-almost.ch.cam.ac.uk/site) | all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations. |
-| [Amber](http://ambermd.org) | A set of molecular mechanical force fields for the simulation of biomolecules |
 | [BCFtools](http://www.htslib.org/) | Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants |
 | [bcl2fastq2](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html) | bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. |
 | [BWA](http://bio-bwa.sourceforge.net/) | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |