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TreeHugger - 0.5

Constructing NJ trees from DNA and Protein alignments.

TreeHugger is a simple tool for constructing NJ trees from DNA and Protein alignments.

Paste in multiple alignment (DNA or Protein) in FASTA, ALN or MSF format.

Upload multiple alignment (DNA or Protein) in FASTA, ALN or MSF format.

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Tree hugger (placeholder)
View example alignment files

Instructions: Paste in or upload a multiple alignment of DNA or Protein sequences (FASTA, ALN or MSF format) and hit submit.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.

CITATIONS

For publication of results, please cite:
Rasmus Wernersson & Anders Gorm Pedersen
TreeHugger - your friendly local neighborhood tree builder.
(in preparation)

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 file format and whether the sequences are DNA or Protein, and construct a phylogenetic tree using the NJ algorithm.

The results are shown in the standard Newick/PHYLIP 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

GETTING HELP

If you need help regarding technical issues (e.g. errors or missing results) contact Technical Support. Please include the name of the service and version (e.g. NetPhos-4.0). If the error occurs after the job has started running, please include the JOB ID (the long code that you see while the job is running).

If you have scientific questions (e.g. how the method works or how to interpret results), contact Correspondence.

Correspondence: Technical Support: