Online sequence alignment programs

Save Translated alignment as Amino acids nucleotide dataset only : Program will translate nucleotides into AminoAcids taking into account user specified edits in codon positions when translating Start debug: Prints more messages Show message log: Displays program messages and errors in a message window Edit: When opening very large files and they are indexed, then the editing capabilities are very limited - but if you need to edit it might be possible if you increase the Memory resources for AliViev see here.

Delete all gaps in all sequences: Degap the whole alignment. Replace terminal GAPs into missing char? Replace missing char?

Example list in clipboard: Woodsia Athyrium Dryopteris Merge two selected sequences: If there is a non-identical overlap AliView will create a consensus sequence. Select charset: If the alignment file has charsets defined you can select one. Tools: Primer: Find primer in current selection: Note - You can change the essential parameters when searching for primers in the Find primer settings 1.

External commands: Edit external commands: You can have AliView call other programs with the current alignment as a parameter see here for examples how to design a command Help menu Help AliView will open this document from this menu Load more sequences from file If you have opened a large file and all sequences were not indexed at once, this menu will show up and you can select other parts of the file to index. You can also change the number of sequences to index at once in the Program preferences, General settings Memory settings If you want AliView to read larger alignments in memory and not from file this allows for more editing capabilities , then you can change the maximum memory settings for the program.

The amount of memory needed for a file to be read into memory is about 2 x file size. Override default program font size on some computers with extreme resolution it might be hard to read text with default settings - OBS!

More sequences are being indexed as they are being viewed. Number of sequences to count when calculating ClustalX consensus on large files it would take very long time to calculate consensus considering every position in a large file Find Primer settings Program to use for "Align all" commands In the Program field you enter the program you want to execute when using the alignment functions in AliView.

Each line is executed as a separate command waiting for the previous to have finished. An an example of this would be a simple combination of commands that take the current alignment and run it in FastTree to create a Maximum Likelihood Tree and finally open the resulting tree in FigTree.

The program FastTree. Move whole unpacked dir: sudo mv jre1. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.

DiAlign-Tx protein. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN.

However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities a Category: DNA alignment , Genomics software. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots.

JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly s Compare gene order between two small bacterial genomes Gene Context Tool. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences.

MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. The Lagan Tookit is a set of alignment programs for comparative genomics. All three are based on the CHAOS local alignment tool and combine speed regions up to several megabases can be aligned in minutes with high accuracy.

An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer. Magnolia is an advanced multiple alignment program suite for nucleic sequences. It's based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. The sequences can be small mitochondrial genomes or large genomic regions up to megabases long.

The MAVID server integrates MAVID with various phylogenetic tree construction programs and visualization tools to allow biomedical researchers who have a collection of related genomic sequences to rapidly identify conserved regions for further analysis. RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment. Spidey is an mRNA-to-genomic alignment program.

Spidey - aligns one or more mRNA sequences to a single genomic sequence. Splign - is a utility for computing cDNA-to-Genomic alignments based on a variation of the Needleman-Wunsch algorithm combined with Blast for compartment detection and greater performance. Splign is accurate in determining splice sites and tolerant to sequencing errors.

JCM Metschnikowia sp. M2Y3 Metschnikowia sp. UWOPS JA9 Micoletzkya japonica Micractinium conductrix Micractinium conductrix Microbotryum intermedium Microbotryum lychnidis-dioicae Microbotryum lychnidis-dioicae p1A1 Lamole Microbotryum saponariae Microbotryum silenes-acaulis Microbotryum silenes-dioicae Microbotryum violaceum Microcaecilia unicolor Microcebus griseorufus Microcebus mittermeieri Mittermeier's mouse lemur Microcebus murinus Gray mouse lemur Microcebus ravelobensis Microcebus sp.

ASPa Micromonas sp. SAG5 Micromonas sp. SAG6 Micromonas sp. SAG7 Micromonas sp. SAG8 Micronycteris hirsuta Microplitis demolitor Micropterus floridanus Florida bass Microsporum canis Microthlaspi erraticum Microtus agrestis Short-tailed field vole Microtus arvalis Common vole Microtus ochrogaster Prairie vole Microtus oeconomus Root vole Middelhovenomyces tepae Miichthys miiuy Mi-iuy croaker Mikania micrantha Millerozyma acaciae Millerozyma farinosa Mimosa pudica Miniopterus natalensis Miniopterus schreibersii Schreibers' long-fingered bat Mirounga angustirostris Northern elephant seal Mirza coquereli Coquerel's mouse lemur Mirza zaza Miscanthus sacchariflorus Mitosporidium daphniae Mixia osmundae Mixornis gularis Striped tit-babbler Mizuhopecten yessoensis Yesso scallop Mnemiopsis leidyi Sea walnut Mochlonyx cinctipes Modiolus philippinarum Moelleriella libera Moesziomyces antarcticus Moesziomyces aphidis Moesziomyces sp.

F16C1 Moesziomyces sp. CRB Monosporascus sp. GIB2 Monosporascus sp. MCB Monosporascus sp. MG Monosporascus sp. PBb Mycosphaerella sp. Ston1 Mycosphaerelloides madeirae Myocastor coypus Nutria Myodes glareolus Bank vole Myotis brandtii Brandt's bat Myotis davidii Myotis lucifugus Little brown bat Myotis myotis Myoxocephalus scorpius Shorthorn sculpin Myriosclerotinia curreyana Myriosclerotinia duriaeana Myriosclerotinia scirpicola Myripristis jacobus Blackbar soldierfish Myripristis murdjan Pinecone soldierfish Myrmecophaga tridactyla Giant anteater Mytilus galloprovincialis Mediterranean mussel Myzus persicae Green peach aphid Nadsonia fulvescens Nadsonia starkeyi-henricii Naegleria fowleri Naegleria gruberi Naegleria lovaniensis Naematelia encephala Naganishia albida Naja naja Indian cobra Nakaseomyces bacillisporus Nakaseomyces delphensis Nakataea oryzae Nakazawaea holstii Nakazawaea peltata Nakazawaea wickerhamii Nanger granti Grant's gazelle Nannizzia gypsea Nannizzia gypsea CBS Nannochloris sp.

RS Nannochloris sp. B Neelides sp. ERTm5 Nematostella vectensis Starlet sea anemone Nemopilema nomurai Neoboletus brunneissimus Neoboletus magnificus Neobulgaria alba Neocallimastix californiae Neodiprion lecontei Redheaded pine sawfly Neodiprion pinetum White pine sawfly Neofusicoccum cordaticola Neofusicoccum kwambonambiense Neofusicoccum parvum Neofusicoccum ribis Neofusicoccum umdonicola Neogale vison American mink Neogobius melanostomus Round goby Neolamprologus brichardi Neolecta irregularis Neolentinus lepideus Neomonachus schauinslandi Hawaiian monk seal Neonectria ditissima Neonectria hederae Neonectria punicea Neonectria sp.

DH2 Neoniphon sammara Sammara squirrelfish Neonothopanus nambi Neopelma chrysocephalum Saffron-crested tyrant-manakin Neophocaena asiaeorientalis Neoporphyra haitanensis Neopyropia yezoensis Susabi-nori Neosciurus carolinensis Gray squirrel Neoscytalidium dimidiatum Neospora caninum Neostethus bicornis Neotoma lepida Desert woodrat Neotragus moschatus Suni Neotragus pygmaeus Royal antelope Nephromyces sp. CHSa Neurospora sp. CHSb Neurospora sp.

CHSc Neurospora sp. FGSC Neurospora sp. LNF Neurospora sp. Ophiocordyceps camponoti-rufipedis Ophiocordyceps camponoti-saundersi nom. MCB Oscheius sp. SAG10 Ostreococcus sp. SAG11 Ostreococcus sp. SAG12 Ostreococcus sp. SAG9 Ostreococcus tauri Ostrinia furnacalis Asian corn borer Ostrinia nubilalis European corn borer Otolemur garnettii Small-eared galago Ourebia ourebi Oribi Ovis ammon Argali Ovis aries Sheep Ovis canadensis Bighorn sheep Oxygymnocypris stewartii Oxytricha trifallax Pachycereus pringlei Pachypanchax playfairii Golden panchax Pachypsylla venusta Hackberry petiole gall psyllid Pachysolen tannophilus Paecilomyces fulvus Paecilomyces niveus Paecilomyces penicillatus Paecilomyces variotii Pagrus major Red seabream Palaemon carinicauda Pallidocercospora crystallina Pampus argenteus Silver pomfret Pan paniscus Pygmy chimpanzee Pan troglodytes Chimpanzee Panaeolus cyanescens Panagrellus redivivus Panagrolaimus davidi Panagrolaimus sp.

ES5 Panagrolaimus sp. JU Panagrolaimus sp. PS Panagrolaimus sp. B Parapristionchus giblindavisi Pararge aegeria Specked wood butterfly Parascaris equorum Parascaris univalens Parasitella parasitica Parasponia andersonii Parastagonospora avenae Parastagonospora nodorum Parasteatoda tepidariorum Common house spider Parastrongyloides trichosuri Parasudis fraserbrunneri Paratrypanosoma confusum Paraurostyla sp. CF01 Penicillium sp. CF05 Penicillium sp. HKF2 Penicillium sp. MA Penicillium sp.

SPG-F1 Penicillium sp. SPG-F15 Penicillium sp. D Phialocephala subalpina Phialophora americana Phialophora attinorum Phialophora verrucosa Philaenus spumarius Meadow spittlebug Philantomba maxwellii Maxwell's duiker Phlebiopsis gigantea Phlebopus portentosus Phlebotomus papatasi Phoca vitulina Harbor seal Phocoena phocoena Harbor porpoise Phocoena sinus Vaquita Phodopus sungorus Phoebis sennae Cloudless sulphur butterfly Phoenicopterus ruber American flamingo Phoenix dactylifera Date palm Pholiota adiposa Pholiota microspora Phoma herbarum Phoma sp.

RAV Phoma sp. XZ Phormia regina Black blowfly Phoronis australis Phortica variegata Photinus pyralis Common eastern firefly Phycis blennoides Phycis phycis Phycomyces blakesleeanus Phylloscopus plumbeitarsus Phylloscopus trochiloides Greenish warbler Phylloscopus trochilus Willow warbler Phyllosticta capitalensis Phyllosticta citriasiana Phyllosticta citricarpa Phyllostomus discolor Pale spear-nosed bat Phymanthus crucifer Physaria acutifolia Physaria fendleri Fendler's bladderpod Physaria ovalifolia Physarum polycephalum Physcomitrium patens Physella acuta Physeter catodon Sperm whale Phytomonas francai Phytomonas serpens Phytomonas sp.

Chile5 Phytophthora taxon totara Phytophthora x alni Phytopythium vexans Phytopythium vexans Picea abies Norway spruce Picea engelmannii Engelmann's spruce Picea glauca White spruce Pichia exigua Pichia fermentans Pichia heedii Pichia kluyveri Pichia kudriavzevii Pichia manshurica Pichia membranifaciens Pichia nakasei Pichia norvegensis Pichia occidentalis Pichia terricola Picochlorum sp.

BH Picochlorum sp. E2 Pirottaea palmicola Pirum gemmata Pisolithus microcarpus Pisolithus tinctorius Pistacia vera Pisum sativum Pea Pithecia pithecia White-faced saki Planiliza haematocheilus So-iny mullet Planoprotostelium fungivorum Plasmodiophora brassicae Plasmodium berghei Plasmodium brasilianum Plasmodium chabaudi Plasmodium coatneyi Plasmodium cynomolgi Plasmodium falciparum Malaria parasite P.

Plasmodium sp. DRC-Itaito Plasmodium sp. UM Pleurobrachia bachei Pleurotus citrinopileatus Pleurotus eryngii Pleurotus ostreatoroseus Pleurotus ostreatus Oyster mushroom Pleurotus platypus Pleurotus salmoneostramineus Pleurotus tuber-regium Pleurotus tuoliensis Pleurozium schreberi Plicaturopsis crispa Plodia interpunctella Indianmeal moth Ploettnerulaceae sp.

BSL10 Priacma serrata Priapulus caudatus Priceomyces carsonii Priceomyces castillae Priceomyces haplophilus Priceomyces medius Prillingera fragicola Primates Primula veris Primula vulgaris Prionailurus bengalensis Leopard cat Pristionchus arcanus Pristionchus entomophagus Pristionchus exspectatus Pristionchus fissidentatus Pristionchus japonicus Pristionchus maxplancki Pristionchus mayeri Pristionchus pacificus Pristis pectinata Smalltooth sawfish Procambarus fallax Deceitful crayfish Procambarus virginalis Procapra przewalskii Przewalski's gazelle Procavia capensis Cape rock hyrax Proctacanthus coquilletti Prolemur simus Greater bamboo lemur Proliferodiscus dingleyae Propithecus coquereli Coquerel's sifaka Prorocentrum minimum Prosopis alba Protaetia brevitarsis Proteromonas lacertae Protobothrops flavoviridis Protobothrops mucrosquamatus Protomyces gravidus Protomyces inouyei Protomyces inundatus Protomyces lactucae-debilis Protomyces macrosporus Protomyces pachydermus Protomyces sp.

C29 Protopolystoma xenopodis Protostelium mycophagum Prototheca cutis Prototheca stagnorum Prototheca wickerhamii Prototheca zopfii Prunus avium Sweet cherry Prunus dulcis Almond Prunus mume Japanese apricot Prunus persica Peach Prunus yedoensis Psammomys obesus Fat sand rat Psammoneis japonica Pseudachorutes palmiensis Pseudevernia furfuracea Pseudo-nitzschia multistriata Pseudobourletiella spinata Pseudocercospora eumusae Pseudocercospora fijiensis Pseudocercospora fijiensis Pseudocercospora musae Pseudocercospora pini-densiflorae Pseudochromis fuscus Brown dottyback Pseudococcus longispinus Long-tailed mealybug Pseudocohnilembus persalinus Pseudodiploria strigosa Pseudogymnoascus destructans Pseudogymnoascus destructans Pseudogymnoascus pannorum Pseudogymnoascus sp.

BL Pseudogymnoascus sp. VKM F Pseudogymnoascus sp. Yap Trench Pseudoloma neurophilia Pseudomassariella vexata Pseudomicrostroma glucosiphilum Pseudomyrmex gracilis Pseudonaja textilis Pseudonectria buxi Pseudonectria foliicola Pseudoneuroterus saliens Pseudoperonospora cubensis Pseudoperonospora humuli Pseudophaeomoniella oleicola Pseudopleuronectes yokohamae Marbled flounder Pseudopodoces humilis Tibetan ground-tit Pseudopyrenochaeta lycopersici Pseudorectes ferrugineus Rusty pitohui Pseudotsuga menziesii Douglas-fir Pseudoturritis turrita Pseudozyma flocculosa Pseudozyma hubeiensis Pseudozyma sp.

DS3sAY3a Pyrenochaeta sp. UM Pyrenophora seminiperda Pyrenophora teres Pyrenophora teres f. CBS Pyronema omphalodes Pyrrhoderma noxium Pyrrhoderma noxium Pyrrhura frontalis Maroon-bellied parakeet Pyrrhura griseipectus Gray-breasted parakeet Pyrus betulifolia Pyrus ussuriensis x Pyrus communis Pyrus x bretschneideri Chinese white pear Pythium aphanidermatum Pythium arrhenomanes Pythium brassicum Pythium guiyangense Pythium insidiosum Pythium oligandrum Pythium periplocum Python bivittatus Burmese python Pyxicephalus adspersus Quambalaria eucalypti Quercus lobata Quercus robur Quercus suber Quillaja saponaria Rachicladosporium antarcticum Rachicladosporium monterosium Rachicladosporium sp.

KR Rhagoletis zephyria Snowberry fruit fly Rhamnella rubrinervis Rhamphochromis esox Rhazya stricta Rhea americana Greater rhea Rhea pennata Rhinatrema bivittatum Two-lined caecilian Rhincodon typus Whale shark Rhinella marina Marine toad Rhinocladiella mackenziei Rhinolophus ferrumequinum Greater horseshoe bat Rhinolophus sinicus Chinese rufous horseshoe bat Rhinopithecus bieti Black snub-nosed monkey Rhinopithecus roxellana Golden snub-nosed monkey Rhipicephalus microplus Southern cattle tick Rhizaria sp.

AMa Rhizopogon vesiculosus Rhizopogon villosulus Rhizopogon vinicolor Rhizopogon vulgaris Rhizopus arrhizus Rhizopus azygosporus Rhizopus delemar Rhizopus microsporus Rhizopus stolonifer Rhodamnia argentea Rhodnius prolixus Rhododendron williamsianum Rhodoleia championii Rhodotorula diobovata Rhodotorula glutinis Rhodotorula graminis Rhodotorula kratochvilovae Rhodotorula mucilaginosa Rhodotorula paludigena Rhodotorula sp.

FNED Rhodotorula sp. JG-1b Rhodotorula sp. MG48 Russula virescens Rutstroemia sp.