彭司实验室

Coronavirus Resources

Metagenomics Resources

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General software ||

Protein related ||

Nucleotide related ||

Molecular evolution ||

Protein residue network ||

Antiviral drug design ||

Antibody database

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Linux or windows software
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There are aligment methods，

The one is align first, then make a tree file
the format of the tree is Newick format, ）

muscle -in mouse_J.pro -out mouse_J.pro.a

muscle -maketree -in mouse_J.pro.a -out mouse_J.phy

Thr other one is aligning to make a aln format file, then make a tree file using other softwarephyml or phylip）.

muscle -in mouse_J.pro -clwout seqs.aln

It is aln format alignment file, and thsi format is popular.

The third alignment method:
Output phy format comparison file.

muscle -in mouse_J.pro -physout seqs.phy

How to refine the alignment results?

muscle -in msa.afa -out refined_msa.afa -refine

How to merge the two alignments results?

muscle -profile -in1 one.afa -in2 two.afa -out both.afa

How to merge a sequence data into the alreadyalignment results?

muscle -profile -in1 existing_msa.afa -in2 new_seq.fa -out combined.afa

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Online Software
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Clustal Omega （For preotein alignment）

MUSCLE （for DNA）

MAFFT （for DNA）

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ClustalW
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ClustalW

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T-Coffee
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T-Coffee

Our Focus

We take S protein as the research focus and take coronavirus recombination as the exploration direction.