EZpipe Instructions
EZpipe processes protein-coding gene datasets to generate standardized alignments and partition files for phylogenetic analyses.
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Validate input FASTA files
- check for duplicate sequences
- verify sequence length consistency
- validate IUPAC characters
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Clean nucleotide sequences
- remove gaps
- detect and remove internal stop codons using a user-defined genetic code
- Translate nucleotide sequences into amino acids
- Align amino acid sequences using MAFFT
- Back-translate amino-acid alignments preserving codon structure
- Trim alignments using Gblocks with codon-aware masking
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Optionally filter codon positions
- retain first and second codon positions only
- or retain all three codon positions
- Concatenate all processed genes into a single supermatrix
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Generate phylogenetic-ready outputs
- PHYLIP alignment file
- PartitionFinder configuration file with codon-based partitions
EZpipe covers all manually intensive preprocessing steps but does not perform phylogenetic inference. For tree reconstruction, we recommend external services such as Galaxy Server.
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Upload FASTA files. Acceptable formats are:
.fasta, .fa, .fsa, .fas, .fna, .ffn, .faa, .frn - Each FASTA file must correspond to a single genetic marker and be named accordingly.
- Please ensure that:
- only FASTA files are uploaded;
- taxon names are consistent across genes;
- sequences contain valid nucleotides only ( IUPAC ambiguity codes allowed );
- internal gaps are absent (they will be removed if detected).
Upload Your Files
*If not provided, a random job ID will be assigned.