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Verdant

A database-driven suite of tools for annotation, alignment, and tree estimation of chloroplast genomes in a web-based platform. Verdant provides a number of key features designed for usability, including: automated annotation of both whole and partial plastomes for protein coding genes, phylogeny estimation, annotation visualization and downloadable datasets of aligned and unaligned plastome region. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware.

GeSeq

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Generates high-quality annotations in a default mode using a curated reference gene set. GeSeq enables user to upload proprietary, most up to-date or novel feature-containing reference sets. This tool urges user to curate gene annotations that failed or are particularly tricky as well as tiny exons or rapidly evolving genes. It can show independent annotations by the best-matching reference sequences and its corresponding profile Hidden Markov Model (HMM) hit or third party tRNA annotators.

CpGAVAS

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Allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. CpGAVAS will become an indispensable tool for researchers studying chloroplast genomes.