A command-line tool that analyses the diversity and motifs of biological sequences

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Project links

Source Code

Project description

DiMA - Diversity Motif Analyser

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What is DiMA?
Installation
Basic Usage
Advance Usage
Command-Line Arguments
Module Parameters

What is DiMA?

Protein sequence diversity is one of the major challenges in the design of diagnostic, prophylactic and therapeutic interventions against viruses. DiMA is a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses. DiMA provides a quantitative measure of sequence diversity by use of Shannon’s entropy, applied via a user-defined k-mer sliding window. Further, the entropy value is corrected for sample size bias by applying a statistical adjustment. Additionally, DiMA further interrogates the diversity by dissecting the entropy value at each k-mer position to various diversity motifs. The distinct k-mer sequences at each position are classified into the following motifs based on their incidence.

Index: The predominant sequence.
Major: The sequence with the second highest incidence after the Index.
Minor: Kmers with incidence in between major and unique motifs
Unique: Kmers which are only seen once in a particular kmer position.

Moreover, the description line of the sequences in the alignment can be formatted for inclusion of meta-data that can be tagged to the diversity motifs. DiMA enables comparative diversity dynamics analysis, within and between proteins of a virus species, and proteomes of different viral species.

Installation

pip install dima-cli

Basic Usage

Shell Command

dima-cli -i aligned_sequences.afa -o results.json

Python

from dima import Dima
results = Dima(sequences="aligned_sequences.afa").run()

Results

Click to view basic results

{
  "sequence_count": 5,
  "support_threshold": 30,
  "low_support_count": 20,
  "sample_name": "Unknown Sample",
  "kmer_length": 9,
  "results": [
    {
      "position": 1,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "MSASKEIKS",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "SAGVYMGNL",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 2,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "AGVYMGNLS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "SASKEIKSF",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 3,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "GVYMGNLSS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "ASKEIKSFL",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 4,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "VYMGNLSSQ",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "SKEIKSFLW",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 5,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "KEIKSFLWT",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "YMGNLSSQQ",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 6,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "MGNLSSQQL",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "EIKSFLWTQ",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 7,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "IKSFLWTQS",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "GNLSSQQLD",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 8,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "KSFLWTQSL",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "NLSSQQLDQ",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 9,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "SFLWTQSLR",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "LSSQQLDQR",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 10,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "SSQQLDQRR",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "FLWTQSLRR",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 11,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "LWTQSLRRE",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "SQQLDQRRA",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 12,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "QQLDQRRAL",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "WTQSLRREL",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 13,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "TQSLRRELS",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "QLDQRRALL",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 14,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "QSLRRELSG",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "LDQRRALLS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "QSLRRELSS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 15,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "DQRRALLSM",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "SLRRELSGY",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "SLRRELSSY",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 16,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "QRRALLSMI",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "LRRELSSYC",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "LRRELSGYC",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 17,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "RRELSGYCS",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "RRALLSMIG",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "RRELSSYCS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 18,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "RELSGYCSN",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "RALLSMIGM",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "RELSSYCSN",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    },
    {
      "position": 19,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "ALLSMIGMS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "ELSSYCSNI",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "ELSGYCSNI",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        }
      ]
    },
    {
      "position": 20,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "LSGYCSNIK",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": null
        },
        {
          "sequence": "LLSMIGMSG",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        },
        {
          "sequence": "LSSYCSNIK",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": null
        }
      ]
    }
  ]
}

Advance Usage

Shell Command

dima-cli -i aligned_sequences.afa -o results.json -f "accession|strain|country|date"

Python

from dima import Dima
results = Dima(sequences="aligned_sequences.afa", header_format="accession|strain|country|date").run()

Results

Click to view advanced results

{
  "sequence_count": 5,
  "support_threshold": 30,
  "low_support_count": 20,
  "sample_name": "Unknown Sample",
  "kmer_length": 9,
  "results": [
    {
      "position": 1,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "MSASKEIKS",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "Accession": {
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75321.1": 1,
              "AYD75325.1": 1
            },
            "Country": {
              "Sierra Leone": 4
            },
            "Species": {
              "Homo sapiens": 3,
              "Unknown": 1
            },
            "Year": {
              "1977": 1,
              "2012": 1,
              "1980": 1,
              "1979": 1
            }
          }
        },
        {
          "sequence": "SAGVYMGNL",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Accession": {
              "AYD75329.1": 1
            },
            "Country": {
              "Sierra Leone": 1
            },
            "Year": {
              "1975": 1
            },
            "Species": {
              "Homo sapiens": 1
            }
          }
        }
      ]
    },
    {
      "position": 2,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "SASKEIKSF",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "Species": {
              "Homo sapiens": 3,
              "Unknown": 1
            },
            "Year": {
              "1977": 1,
              "1980": 1,
              "1979": 1,
              "2012": 1
            },
            "Country": {
              "Sierra Leone": 4
            },
            "Accession": {
              "AYD75325.1": 1,
              "QEP52131.1": 1,
              "AYD75365.1": 1,
              "AYD75321.1": 1
            }
          }
        },
        {
          "sequence": "AGVYMGNLS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Species": {
              "Homo sapiens": 1
            },
            "Year": {
              "1975": 1
            },
            "Accession": {
              "AYD75329.1": 1
            },
            "Country": {
              "Sierra Leone": 1
            }
          }
        }
      ]
    },
    {
      "position": 3,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "ASKEIKSFL",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "Year": {
              "1980": 1,
              "1977": 1,
              "1979": 1,
              "2012": 1
            },
            "Accession": {
              "AYD75321.1": 1,
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75325.1": 1
            },
            "Country": {
              "Sierra Leone": 4
            },
            "Species": {
              "Unknown": 1,
              "Homo sapiens": 3
            }
          }
        },
        {
          "sequence": "GVYMGNLSS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Accession": {
              "AYD75329.1": 1
            },
            "Species": {
              "Homo sapiens": 1
            },
            "Country": {
              "Sierra Leone": 1
            },
            "Year": {
              "1975": 1
            }
          }
        }
      ]
    },
    {
      "position": 4,
      "low_support": "LS",
      "entropy": 0.7219280948873623,
      "support": 5,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 100.0,
      "total_variance": 20.0,
      "diversity_motifs": [
        {
          "sequence": "SKEIKSFLW",
          "count": 4,
          "incidence": 80.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "Accession": {
              "AYD75325.1": 1,
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75321.1": 1
            },
            "Country": {
              "Sierra Leone": 4
            },
            "Species": {
              "Unknown": 1,
              "Homo sapiens": 3
            },
            "Year": {
              "2012": 1,
              "1979": 1,
              "1980": 1,
              "1977": 1
            }
          }
        },
        {
          "sequence": "VYMGNLSSQ",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Accession": {
              "AYD75329.1": 1
            },
            "Year": {
              "1975": 1
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          "motif_long": "Unique",
          "metadata": {
            "Accession": {
              "QEP52131.1": 1
            },
            "Species": {
              "Homo sapiens": 1
            },
            "Country": {
              "Sierra Leone": 1
            },
            "Year": {
              "2012": 1
            }
          }
        },
        {
          "sequence": "ALLSMIGMS",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Country": {
              "Sierra Leone": 1
            },
            "Accession": {
              "AYD75329.1": 1
            },
            "Species": {
              "Homo sapiens": 1
            },
            "Year": {
              "1975": 1
            }
          }
        }
      ]
    },
    {
      "position": 20,
      "low_support": "LS",
      "entropy": 1.3709505944546687,
      "support": 5,
      "distinct_variants_count": 2,
      "distinct_variants_incidence": 100.0,
      "total_variance": 40.0,
      "diversity_motifs": [
        {
          "sequence": "LLSMIGMSG",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Accession": {
              "AYD75329.1": 1
            },
            "Country": {
              "Sierra Leone": 1
            },
            "Species": {
              "Homo sapiens": 1
            },
            "Year": {
              "1975": 1
            }
          }
        },
        {
          "sequence": "LSGYCSNIK",
          "count": 3,
          "incidence": 60.000004,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "Country": {
              "Sierra Leone": 3
            },
            "Year": {
              "1979": 1,
              "1977": 1,
              "1980": 1
            },
            "Accession": {
              "AYD75365.1": 1,
              "AYD75321.1": 1,
              "AYD75325.1": 1
            },
            "Species": {
              "Unknown": 1,
              "Homo sapiens": 2
            }
          }
        },
        {
          "sequence": "LSSYCSNIK",
          "count": 1,
          "incidence": 20.0,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "Year": {
              "2012": 1
            },
            "Species": {
              "Homo sapiens": 1
            },
            "Accession": {
              "QEP52131.1": 1
            },
            "Country": {
              "Sierra Leone": 1
            }
          }
        }
      ]
    }
  ]
}

Command-Line Arguments

Argument	Type	Required	Default	Example	Description
-h	N/A	False	N/A	`dima-cli -h`	Prints a summary of all available command-line arguments.
-n	String	False	Unknown	`dima-cli -i sequences.afa -o results.json -f "accession\	strain\
-v	N/A	False	N/A	`dima-cli -v`	Prints the version of dima-cli that is currently installed.
-p	String	False	Unknown Sample	`dima-cli -n "Coronavirus Surface Protein" -i sequences.afa -o results.json`	The name of the sample that will appear on the results.
-i	String	True	N/A	`dima-cli -i sequences.afa -o results.json`	The path to the FASTA Multiple Sequence Alignment file.
-o	String	True	N/A	`dima-cli -i sequences.afa -o results,json`	The location where the results shall be saved.
-l	Integer	False	9	`dima-cli -i sequences.afa -l 12 -o results.json`	The length of the kmers generated.
-f	String	False	N/A	`dima-cli -i sequences.afa -f "accession\	strain\
-s	Integer	False	30	`dima-cli -i sequences.afa -l 12 -s 40 -o results.json`	The minimum required support for each kmer position.
-a	nucleotide/protein	False	protein	`dima-cli -i dna_sequences.afa -a nucleotide -o results.json`	The alphabet of the sequences (ie: `protein`/`nucleotide`, default: protein)
-t	json/xlsx	False	json	`dima-cli -i dna_sequences.afa -a nucleotide -o results.json -t xlsx`	The output format (ie: `json`/`xlsx`, default: json)
-c	String	False	N/A	`dima-cli -i dna_sequences.afa -a nucleotide -o results.json -c hcs.json`	Path to save Highly Conserved Sequences (HCS) in JSON format.
-e	Integer	False	None	`dima-cli -i dna_sequences.afa -a nucleotide -o results.json -c hcs.json -e 200`	Threshold for HCS concatenation.

Module Parameters

Parameter	Type	Required	Default	Description
sequences	String/StringIO	True	N/A	The path to a FASTA Multiple Sequence Alignment file (MSA), or a StringIO object containing FASTA MSA.
kmer_length	Integer	False	9	The length of the kmers generated.
header_fillna	String	False	Unknown	Silently fix missing values in the FASTA header with given value (only required when `header_format` is given).
header_format	String	False	N/A	The format of the FASTA header. Labels where each variant of a kmer position originated from.
support_threshold	Integer	False	30	The minimum required support for each kmer position.
sample_name	String	False	Unknown Sample	The name of the sample that will appear on the results.
alphabet	String	False	protein	The alphabet of the sequences (ie: protein/nucleotide, default: protein)

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