phyloBARCODER: Plants

(1) Anonymous sequences

Examples:

(Pinus reference sequences).

>Brennan2019_SRR7289008.356
AAGTGTTGGATTCAAAGCTGGTGTTAAAGATTATAAATTGACTTATTACACTCCTGAATATGAAACCAAAGATACTGATATCTTAGCAGCATTTCGAGTAACTCCTCAACCTGGAGTTCCCCCTGAAGAAGCAGGGGCTGCGGTAGCTGCGGAATCTTCTACTGGTACCTGGACAACTGTATGGACTGACGGGCTTACAAGTCTTGATCGCTACAAAGGTCGATGCTACCACATTGAGCCTGTTGCTGGCGAAGAAAGTCAATTTATTGCTTATGTAGCGTACCCCTTAGACCTTTTTGAGGAAGGTTCTGTCACTAACATGTTTACTTCCATTGTGGGTAATGTATTTGGGTTCAAGGCCCTGCGCGCTCTACGTTTGGAAGATTTGCGAATCCCTCCTGCTTACACTAAAACTTTCCAAGGCCCACCTCACGGTATCCAAGTTGAGAGAGATAAAT
>Brennan2019_SRR7289008.4136
AAGTGCTGGATTCAAAGCTGGTGTTAAAGATTACAAATTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCTGGAGTTCCACCTGAAGAAGCAGGGGCCGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTGTGGACTGATGGACTTACCAACCTTGATCGTTACAAAGGGCGATGCTACCACATCGAGCCCGTTGCTGGAGAAGAAAGTCAATTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCCATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAAGATCTGCGAATTCCTGTTGCTTATGTTAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAGAGAGATAAAT
>Brennan2019_SRR7288995.499
TAGTGTCGGATTCAAAGCTGGTGTTAAAGATTACAGATTAACTTATTATACTCCTGAATATCAGACCAAAGATACAGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGGGTGCCACCTGAAGAAGCGGGAGCAGCAGTAGCTGCTGAATCTTCCACCGGTACATGGACCACTGTTTGGACCGATGGACTTACTAGTCTCGATCGTTACAAGGGGCGATGCTATGACATCGAACCCGTTCCTGGAGAGGAGACTCAATTTATTGCCTATGTAGCTTACCCCTTAGACCTTTTCGAAGAAGGTTCTGTTACTAACTTGTTCACTTCCATTGTAGGTAATGTATTTGGATTCAAGGCCCTACGGGCTCTACGTTTGGAAGATTTGCGGATTCCCCCTGCTTATTCCAAAACTTTTCAGGGTCCACCTCATGGTATCCAAGTTGAAAGAGATAAAT
>Brennan2019_SRR7288995.5
TAGTGTCGGATTCAAAGCTGGTGTTAAAGATTACAGATTAACTTATTATACTCCTGAATATCAGACCAAAGATACAGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGGGTGCCACCTGAAGAAGCGGGAGCAGCAGTAGCTGCTGAATCTTCCACCGGTACATGGACCACTGTTTGGACCGATGGACTTACTAGTCTCGATCGTTACAAGGGGCGATGCTATGACATCGAGCCCGTTCCTGGAGAGGAGACTCAATTTATTGCCTATGTAGCTTACCCCTTAGACCTTTTCGAAGAAGGTTCTGTTACTAACTTGTTCACTTCCATTGTAGGTAATGTATTTGGATTCAAGGCCTTACGGGCTCTACGTTTGGAAGATTTGCGGATTCCCCCTTCTTATTCCAAAACTTTTCAGGGTCCACCTCATGGTATCCAAGTTGAAAGAGATAAAT
>Brennan2019_SRR7288995.2985
AAGTGTTGGATTCAAAGCCGGTGTTAAAGATTATAAATTGACTTATTATACTCCTGACTATGTAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCCGGGGTTCCGCCCGAGGAAGCCGGGGCCGCGGTAGCTGCGGAATCTTCTACTGGTACATGGACAACTGTGTGGACCGATGGGCTTACCAGCCTTGATCGTTATAAAGGACGATGCTACAACATTGAGCCCGTTGCTGGAGAAGAAAATCAATATATATGTTATGTAGCTTACCCTTTAGACCTTTTTGAAGAGGGTTCTGTTACTAACATGTTTACTTCCATTGTGGGTAATGTATTTGGGTTTAAAGCCCTGCGCGCTCTACGTCTAGAGGATCTACGAATCCCTCCCGCGTATTCGAAAACTTTCCAAGGCCCCCCTCATGGCATCCAAGTTGAGAGAGATAAAT
>Brennan2019_SRR7289008.29
AAGTGTTGGATTTCAAGCTGGTGTTAAAGATTATAAATTGACTTACTACACCCCGGAGTATGAAACCAAGGATACTGATATCTTGGCAGCATTTCGAGTAACTCCTCAGCCTGGGGTTCCGCCGGAAGAAGCAGGGGCTGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACCAGTCTTGATCGTTACAAAGGACGATGCTATCACATCGAGCCTGTTGCTGGGGAAGACAACCAATGGATCTGTTATGTAGCTTATCCATTAGACCTATTTGAAGAAGGTTCCGTTACTAACATGTTTACTTCCATTGTGGGTAACGTATTTGGTTTCAAAGCCCTACGTGCTCTACGTCTGGAAGATCTACGAATTCCCCCTGCTTATTCAAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAAAGAGATAAGT
>Brennan2019_SRR7289008.105
AAGTGTTGGATTTCAAGCTGGTGTTAAAGATTATAAATTGACTTACTACACCCCGGAGTATGAAACCAAGGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAGCCTGGGGTTCCGCCGGAAGAAGCAGGGGCTGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACCAGTCTTGATCGTTACAAAGGACGATGCTATCATATCGAGCCTGTTGCTGGGGAAGACAACCAATGGATCTGTTATGTAGCTTATCCATTAGACCTATTTGAAGAGGGTTCCGTTACTAACATGTTTACTTCTATTGTGGGTAACGTATTTGGTTTCAAAGCCCTACGTGCTCTACGTCTGGAGGATCTACGAATTCCCGTTGCTTATTCAAAAACTTTCCAAGGTCCGCCTCATGGTATCCAAGTTGAAAGAGATAAGT
>Brennan2019_SRR7289008.234
AAGTGTTGGATTTCAAGCTGGTGTTAAAGATTATAAATTGACTTACTACACTCCGGAGTATGAAACCAAGGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAGCCTGGGGTTCCCCCGGAAGAAGCAGGGGCTGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACCAGTCTTGATCGTTACAAAGGACGATGCTATCACATCGAGCCTGTTGCTGGGGAAGACAACCAATGGATCTGTTATGTAGCTTATCCATTAGACCTATTTGAAGAGGGTTCCGTTACTAACATGTTTACTTCCATTGTGGGTAACGTATTTGGTTTCAAAGCCCTACGTGCTCTACGTCTGGAGGATCTACGAATTCCCGTTGCTTATGCAAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAAAGAGATAAGT
>Brennan2019_SRR7289008.237
AAGTGTTGGATTCAAAGCTGGTGTTAAAGATTATAAACTGACTTATTATACTCCTGACTATGAAACCAAAGATACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAACCTGGAGTTCCTCCTGAGGAAGCAGGGGCTGCGGTAGCTGCTGAATCTTCTACTGGTACATGGACAACTGTGTGGACCGATGGGCTTACCAGCCTTGATCGTTATAAAGGAAGATGCTACCACATCGAGCCTGTTGCTGGAGACGAAAATCAATATATATGTTATGTAGCTTACCCTTTAGACCTTTTTGAAGAAGGTTCTGTTACTAATATGTTTACTTCCATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGCGCTCTACGTCTGGAGGATCTGCGAATCCCTACTTCCTATACGAAAACTTTCCAAGGCCCGCCTCATGGCATCCAAGTTGAGAGAGATAAAT
>Brennan2019_SRR7289008.524
AGGTGTTGGATTCAAAGCTGGTGTTAAAGAATACAAATTGACTTATTATACTCCTGACTATGAACCCCATGACCATGATATCTTGGCAGCATTTCGAGTAACTCCTCAACCTGGAGTTCCACCAGAAGAAGCAGGGGCCGCGGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTGTGGACCGATGGACTTACCAGCCTTGATCGTTACAAAGGACGATGCTACCACATCGAGCCTGTTCCTGGAGAAGAAAGTCAGTTTATTGCTTATGTAGCTTACCCATTAGACCTTTTTGAAGAAGGTTCTGTTACTAACATGTTTACTTCCATTGTGGGTAATGTATTTGGGTTCAAAGCCCTGCGTGCTCTACGTTTGGAGGATTTGCGAATCCCTCCTGCTTATACGAAAACTTTCCAAGGCCCGCCTCATGGTATCCAAGTTGAAAGAGATAAAT

Or load a FASTA file

Number of queries

(2) Databases

Anonymous DB (input sequences)

Hits for each query sequence

E-value threshold

Pre-installed DB: Plant rbcL

Reference database

Plant chloroplast rbcL references: 87,270 original reference sequences from Bell et al. (2017), extended with FTOL and Kuo data to include 6,831 fern sequences (FTOL v1.9.0; Kuo et al., 2024). This combined library is not a complete inventory of world plants.

References: Bell (2016) data, Bell et al. (2017) (CC BY 4.0; modifications); FTOL (Nitta et al., 2022) and Kuo et al. (2024) (CC0).

Hits for each query sequence

E-value threshold

User DB (optional)

Reference sequences in FASTA format
Use the same marker region as the query sequences.

Hits for each query sequence

E-value threshold

(3) Measure of confidence

Bootstrap analysis: branch support

Tree Identification (rbcL)

(1) Anonymous sequences

(2) Databases

Anonymous DB (input sequences)

Pre-installed DB: Plant rbcL

User DB (optional)

(3) Measure of confidence

Sequence Extraction