Usage instructions

Quick start

Paste in a DNA or Protein multiple alignment in FASTA, ALN or MSF format, and hit "Submit query". TreeHugger will then autodetect fileformate and whether the sequences are DNA or Protein, and construct a phylogenetic tree using the NJ algorith.

The result are shown in the standard Newick/PHYLYP format for further visualization in a tree viewer - e.g. FigTree.

Example data

Sample DNA alignment

The following alignment in FASTA format is a set of Alpha-globin genes from a range for organisms. It was aligned using the RevTrans server (notice that each gap is a multiple of three).

>Sheep 
ATGGCCCTGTGGACACGCCTGGTGCCCCTGCTGGCCCTGCTGGCACTCTG
GGCCCCCGCCCCGGCCCACGCCTTCGTCAACCAGCACCTGTGCGGCTCCC
ACCTGGTGGAGGCGCTGTACCTGGTGTGCGGAGAGCGCGGCTTCTTCTAC
ACGCCCAAGGCCCGCCGGGAGGTGGAGGGCCCCCAGGTGGGGGCGCTGGA
GCTGGCCGGAGGCCCC------GGC---------GCGGGTGGCCTGGAGG
GGCCCCCGCAGAAGCGTGGCATCGTGGAGCAGTGCTGCGCCGGCGTCTGC
TCTCTCTACCAGCTGGAGAACTACTGTAAC
>OwlMonkey 
ATGGCCCTGTGGATGCACCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTG
GGGACCCGAGCCAGCCCCGGCCTTTGTGAACCAGCACCTGTGCGGCCCCC
ACCTGGTGGAAGCCCTCTACCTGGTGTGCGGGGAGCGAGGTTTCTTCTAC
GCACCCAAGACCCGCCGGGAGGCGGAGGACCTGCAGGTGGGGCAGGTGGA
GCTGGGTGGGGGCTCTATCACGGGCAGCCTGCCACCC------TTGGAGG
GTCCCATGCAGAAGCGTGGCGTCGTGGATCAGTGCTGCACCAGCATCTGC
TCCCTCTACCAGCTGCAGAACTACTGCAAC
>Chimp 
ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGTGCTGCTGGCCCTCTG
GGGACCTGACCCAGCCTCGGCCTTTGTGAACCAACACCTGTGCGGCTCCC
ACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTAC
ACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGA
GCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGG
GGTCCCTGCAGAAGCGTGGTATCGTGGAACAATGCTGTACCAGCATCTGC
TCCCTCTACCAGCTGGAGAACTACTGCAAC
>Dog 
ATGGCCCTCTGGATGCGCCTCCTGCCCCTGCTGGCCCTGCTGGCCCTCTG
GGCGCCCGCGCCCACCCGAGCCTTCGTTAACCAGCACCTGTGTGGCTCCC
ACCTGGTAGAGGCTCTGTACCTGGTGTGCGGGGAGCGCGGCTTCTTCTAC
ACGCCTAAGGCCCGCAGGGAGGTGGAGGACCTGCAGGTGAGGGACGTGGA
GCTGGCCGGGGCGCCTGGCGAGGGCGGCCTGCAGCCCCTGGCCCTGGAGG
GGGCCCTGCAGAAGCGAGGCATCGTGGAGCAGTGCTGCACCAGCATCTGC
TCCCTCTACCAGCTGGAGAATTACTGCAAC
>Pig 
ATGGCCCTGTGGACGCGCCTCCTGCCCCTGCTGGCCCTGCTGGCCCTCTG
GGCGCCCGCCCCGGCCCAGGCCTTCGTGAACCAGCACCTGTGCGGCTCCC
ACCTGGTGGAGGCGCTGTACCTGGTGTGCGGGGAGCGCGGCTTCTTCTAC
ACGCCCAAGGCCCGTCGGGAGGCGGAGAACCCTCAGGCAGGTGCCGTGGA
GCTGGGCGGAGGCCTG------GGCGGCCTGCAGGCCCTGGCGCTGGAGG
GGCCCCCGCAGAAGCGTGGCATCGTGGAGCAGTGCTGCACCAGCATCTGT
TCCCTCTACCAGCTGGAGAACTACTGCAAC
>GuineaPig 
ATGGCTCTGTGGATGCATCTCCTCACCGTGCTGGCCCTGCTGGCCCTCTG
GGGGCCCAACACTAATCAGGCCTTTGTCAGCCGGCATCTGTGCGGCTCCA
ACTTAGTGGAGACATTGTATTCAGTGTGTCAGGATGATGGCTTCTTCTAT
ATACCCAAGGACCGTCGGGAGCTAGAGGACCCACAGGTGGAGCAGACAGA
ACTGGGCATGGGCCTGGGGGCAGGTGGACTACAGCCCTTGGCACTGGAGA
TGGCACTACAGAAGCGTGGCATTGTGGATCAGTGCTGTACTGGCACCTGC
ACACGCCACCAGCTGCAGAGCTACTGCAAC
>GreenMonkey 
ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTG
GGGACCTGACCCGGTCCCGGCCTTTGTGAACCAGCACCTGTGCGGCTCCC
ACCTGGTGGAAGCCCTCTACCTGGTGTGCGGGGAGCGAGGCTTCTTCTAC
ACGCCCAAGACCCGCCGGGAGGCAGAGGACCCGCAGGTGGGGCAGGTAGA
GCTGGGCGGGGGCCCTGGCGCAGGCAGCCTGCAGCCCTTGGCGCTGGAGG
GGTCCCTGCAGAAGCGCGGCATCGTGGAGCAGTGCTGTACCAGCATCTGC
TCCCTCTACCAGCTGGAGAACTACTGCAAC
>Human 
ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTG
GGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCAC
ACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTAC
ACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGA
GCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGG
GGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGC
TCCCTCTACCAGCTGGAGAACTACTGCAAC
>Chicken 
ATGGCTCTCTGGATCCGATCACTGCCTCTTCTGGCTCTCCTTGTCTTTTC
TGGCCCTGGAACCAGCTATGCAGCTGCCAACCAGCACCTCTGTGGCTCCC
ACTTGGTGGAGGCTCTCTACCTGGTGTGTGGAGAGCGTGGCTTCTTCTAC
TCCCCCAAAGCCCGACGGGATGTCGAGCAGCCCCTAGTGAGCAGTCCCTT
GCGTGGCGAGGCA---------GGAGTGCTGCCTTTCCAGCAGGAGGAAT
ACGAGAAAGTCAAGCGAGGGATTGTTGAGCAATGCTGCCATAACACGTGT
TCCCTCTACCAACTGGAGAACTACTGCAAC
>Mouse 
ATGGCCCTGTTGGTGCACTTCCTACCCCTGCTGGCCCTGCTTGCCCTCTG
GGAGCCCAAACCCACCCAGGCTTTTGTCAAACAGCATCTTTGTGGTCCCC
ACCTGGTAGAGGCTCTCTACCTGGTGTGTGGGGAGCGTGGCTTCTTCTAC
ACACCCAAGTCCCGCCGTGAAGTGGAGGACCCACAAGTGGAACAACTGGA
GCTGGGAGGAAGCCCC------GGGGACCTTCAGACCTTGGCGTTGGAGG
TGGCCCGGCAGAAGCGTGGCATTGTGGATCAGTGCTGCACCAGCATCTGC
TCCCTCTACCAGCTGGAGAACTACTGCAAC

Sample peptide dataset

The following multiple alignment in ALN (Clustal) format is based on the set of Alpha-globin genes mentioned above. The DNA sequences were translated and aligned using MAFFT via the RevTrans server.

CLUSTAL -  multiple sequence alignment - created by revtrans

Sheep          MALWTRLVPLLALLALWAPAPAHAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEG
OwlMonkey      MALWMHLLPLLALLALWGPEPAPAFVNQHLCGPHLVEALYLVCGERGFFYAPKTRREAED
Chimp          MALWMRLLPLLVLLALWGPDPASAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
Dog            MALWMRLLPLLALLALWAPAPTRAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVED
Pig            MALWTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREAEN
GuineaPig      MALWMHLLTVLALLALWGPNTNQAFVSRHLCGSNLVETLYSVCQDDGFFYIPKDRRELED
GreenMonkey    MALWMRLLPLLALLALWGPDPVPAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
Human          MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
Chicken        MALWIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVEQ
Mouse          MALLVHFLPLLALLALWEPKPTQAFVKQHLCGPHLVEALYLVCGERGFFYTPKSRREVED


Sheep          PQVGALELAGGP--G---AGGLEGPPQKRGIVEQCCAGVCSLYQLENYCN
OwlMonkey      LQVGQVELGGGSITGSLPP--LEGPMQKRGVVDQCCTSICSLYQLQNYCN
Chimp          LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Dog            LQVRDVELAGAPGEGGLQPLALEGALQKRGIVEQCCTSICSLYQLENYCN
Pig            PQAGAVELGGGL--GGLQALALEGPPQKRGIVEQCCTSICSLYQLENYCN
GuineaPig      PQVEQTELGMGLGAGGLQPLALEMALQKRGIVDQCCTGTCTRHQLQSYCN
GreenMonkey    PQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Human          LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Chicken        PLVSSPLRGEA---GVLPFQQEEYEKVKRGIVEQCCHNTCSLYQLENYCN
Mouse          PQVEQLELGGSP--GDLQTLALEVARQKRGIVDQCCTSICSLYQLENYCN